From 1471170104b849439e34ce92e007a711c4d3a0e1 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Wed, 10 Dec 2014 15:32:35 +0000
Subject: [PATCH] [ENSCORESW-1117]. Polyploidy test database extracted from
Triticum aestivum (EG25).
---
.../polyploidy/core/alt_allele.txt | 0
.../polyploidy/core/alt_allele_attrib.txt | 0
.../polyploidy/core/alt_allele_group.txt | 0
.../polyploidy/core/analysis.txt | 49 +
.../polyploidy/core/analysis_description.txt | 48 +
.../polyploidy/core/assembly.txt | 3 +
.../polyploidy/core/assembly_exception.txt | 0
.../polyploidy/core/associated_group.txt | 0
.../polyploidy/core/associated_xref.txt | 0
.../polyploidy/core/attrib_type.txt | 296 +
.../polyploidy/core/coord_system.txt | 4 +
.../polyploidy/core/data_file.txt | 0
.../polyploidy/core/density_feature.txt | 0
.../polyploidy/core/density_type.txt | 7 +
.../polyploidy/core/dependent_xref.txt | 0
.../test-genome-DBs/polyploidy/core/ditag.txt | 0
.../polyploidy/core/ditag_feature.txt | 0
.../t/test-genome-DBs/polyploidy/core/dna.txt | 3 +
.../polyploidy/core/dna_align_feature.txt | 0
.../test-genome-DBs/polyploidy/core/exon.txt | 13 +
.../polyploidy/core/exon_transcript.txt | 13 +
.../polyploidy/core/external_db.txt | 612 +
.../polyploidy/core/external_synonym.txt | 115 +
.../test-genome-DBs/polyploidy/core/gene.txt | 6 +
.../polyploidy/core/gene_archive.txt | 0
.../polyploidy/core/gene_attrib.txt | 6 +
.../polyploidy/core/genome_statistics.txt | 10 +
.../polyploidy/core/identity_xref.txt | 2 +
.../polyploidy/core/interpro.txt | 10218 ++++++++++++++++
.../core/intron_supporting_evidence.txt | 0
.../polyploidy/core/karyotype.txt | 0
.../t/test-genome-DBs/polyploidy/core/map.txt | 0
.../polyploidy/core/mapping_session.txt | 0
.../polyploidy/core/mapping_set.txt | 0
.../polyploidy/core/marker.txt | 0
.../polyploidy/core/marker_feature.txt | 0
.../polyploidy/core/marker_map_location.txt | 0
.../polyploidy/core/marker_synonym.txt | 0
.../test-genome-DBs/polyploidy/core/meta.txt | 115 +
.../polyploidy/core/meta_coord.txt | 4 +
.../polyploidy/core/misc_attrib.txt | 0
.../polyploidy/core/misc_feature.txt | 0
.../polyploidy/core/misc_feature_misc_set.txt | 0
.../polyploidy/core/misc_set.txt | 18 +
.../polyploidy/core/object_xref.txt | 0
.../polyploidy/core/ontology_xref.txt | 0
.../polyploidy/core/operon.txt | 0
.../polyploidy/core/operon_transcript.txt | 0
.../core/operon_transcript_gene.txt | 0
.../polyploidy/core/peptide_archive.txt | 0
.../polyploidy/core/prediction_exon.txt | 0
.../polyploidy/core/prediction_transcript.txt | 0
.../polyploidy/core/protein_align_feature.txt | 0
.../polyploidy/core/protein_feature.txt | 47 +
.../polyploidy/core/repeat_consensus.txt | 17 +
.../polyploidy/core/repeat_feature.txt | 68 +
.../polyploidy/core/seq_region.txt | 6 +
.../polyploidy/core/seq_region_attrib.txt | 9 +
.../polyploidy/core/seq_region_mapping.txt | 0
.../polyploidy/core/seq_region_synonym.txt | 0
.../polyploidy/core/simple_feature.txt | 0
.../polyploidy/core/stable_id_event.txt | 0
.../polyploidy/core/supporting_feature.txt | 0
.../test-genome-DBs/polyploidy/core/table.sql | 887 ++
.../polyploidy/core/transcript.txt | 6 +
.../polyploidy/core/transcript_attrib.txt | 0
.../transcript_intron_supporting_evidence.txt | 0
.../core/transcript_supporting_feature.txt | 0
.../polyploidy/core/translation.txt | 6 +
.../polyploidy/core/translation_attrib.txt | 30 +
.../polyploidy/core/unmapped_object.txt | 0
.../polyploidy/core/unmapped_reason.txt | 51 +
.../test-genome-DBs/polyploidy/core/xref.txt | 0
73 files changed, 12669 insertions(+)
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/alt_allele.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/alt_allele_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/alt_allele_group.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/analysis.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/analysis_description.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/assembly.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/assembly_exception.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/associated_group.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/associated_xref.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/attrib_type.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/coord_system.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/data_file.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/density_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/density_type.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/dependent_xref.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/ditag.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/ditag_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/dna.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/dna_align_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/exon.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/exon_transcript.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/external_db.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/external_synonym.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/gene.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/gene_archive.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/gene_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/genome_statistics.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/identity_xref.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/interpro.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/intron_supporting_evidence.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/karyotype.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/map.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/mapping_session.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/mapping_set.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/marker.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/marker_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/marker_map_location.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/marker_synonym.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/meta.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/meta_coord.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/misc_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/misc_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/misc_feature_misc_set.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/misc_set.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/object_xref.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/ontology_xref.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/operon.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/operon_transcript.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/operon_transcript_gene.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/peptide_archive.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/prediction_exon.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/prediction_transcript.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/protein_align_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/protein_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/repeat_consensus.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/repeat_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/seq_region.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/seq_region_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/seq_region_mapping.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/seq_region_synonym.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/simple_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/stable_id_event.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/supporting_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/table.sql
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/transcript.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/transcript_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/transcript_intron_supporting_evidence.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/transcript_supporting_feature.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/translation.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/translation_attrib.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/unmapped_object.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/unmapped_reason.txt
create mode 100644 modules/t/test-genome-DBs/polyploidy/core/xref.txt
diff --git a/modules/t/test-genome-DBs/polyploidy/core/alt_allele.txt b/modules/t/test-genome-DBs/polyploidy/core/alt_allele.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/alt_allele_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/alt_allele_attrib.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/alt_allele_group.txt b/modules/t/test-genome-DBs/polyploidy/core/alt_allele_group.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/analysis.txt b/modules/t/test-genome-DBs/polyploidy/core/analysis.txt
new file mode 100644
index 0000000000..d2aeee21ca
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/analysis.txt
@@ -0,0 +1,49 @@
+178 2014-11-20 11:21:58 trf \N \N \N trf 4.0 /nfs/panda/ensemblgenomes/external/bin/trf 2 5 7 80 10 40 500 -d -h Bio::EnsEMBL::Analysis::Runnable::TRF \N trf tandem_repeat
+100 2013-08-23 16:08:26 tgac_pred_supp7 \N \N \N \N \N \N \N \N \N \N \N
+177 2014-11-20 11:21:58 dust \N \N \N dustmasker \N /nfs/panda/ensemblgenomes/external/bin/dustmasker \N Bio::EnsEMBL::Analysis::Runnable::DustMasker \N dust repeat_region
+101 2013-08-23 16:08:26 tgac_pred_supp17 \N \N \N \N \N \N \N \N \N \N \N
+119 2013-11-07 15:48:01 mips_taestivum \N \N \N \N \N \N \N \N \N \N \N
+187 2014-11-26 14:53:56 pfam Pfam 27.0 \N pfam \N \N \N \N \N \N \N
+195 2014-11-26 14:54:02 ncoils ncoils \N \N ncoils \N \N \N \N \N \N \N
+186 2014-11-26 14:53:54 hmmpanther PANTHER 9.0 \N hmmpanther \N \N \N \N \N \N \N
+190 2014-11-26 14:53:59 prints PRINTS 42.0 \N prints \N \N \N \N \N \N \N
+200 2014-11-26 14:54:06 interpro2pathway InterPro2Pathway \N \N interpro2pathway \N \N \N \N \N \N \N
+196 2014-11-26 14:54:03 signalp SignalP \N \N signalp \N \N \N \N \N \N \N
+191 2014-11-26 14:53:59 scanprosite Prosite_patterns 20.105 \N scanprosite \N \N \N \N \N \N \N
+45 0000-00-00 00:00:00 wheat_snp_a \N \N \N \N \N \N \N \N \N \N \N
+46 0000-00-00 00:00:00 wheat_snp_b \N \N \N \N \N \N \N \N \N \N \N
+136 2013-11-16 16:36:35 xrefexoneratedna \N \N \N \N \N \N \N \N \N \N \N
+137 2013-11-16 16:36:35 xrefexonerateprotein \N \N \N \N \N \N \N \N \N \N \N
+138 2013-11-16 16:49:20 xrefchecksum \N \N \N \N \N \N \N \N \N \N \N
+140 2014-03-18 00:00:00 ncrna_eg \N \N \N \N \N \N \N \N \N ensemblgenomes gene
+141 2014-05-09 10:51:51 ena ena \N \N \N \N \N \N \N \N ena gene
+142 2014-05-09 10:51:51 gl_xref gl_xref \N \N \N \N \N \N \N \N gl_xref \N
+143 2014-05-09 10:51:52 gl_name_xref gl_name_xref \N \N \N \N \N \N \N \N gl_name_xref \N
+145 2014-05-09 10:52:01 ena_rna ena \N \N \N \N \N \N \N \N ena_rna gene
+146 2014-05-09 10:52:02 ena_gene ena \N \N \N \N \N \N \N \N ena_gene feature
+147 2014-05-09 10:52:02 ena_exon ena \N \N \N \N \N \N \N \N ena_exon feature
+148 2014-11-25 00:00:00 percentgc \N \N \N \N \N \N \N \N \N \N \N
+149 2014-05-09 00:00:00 longnoncodingdensity \N \N \N \N \N \N \N \N \N \N \N
+150 2014-11-25 00:00:00 pseudogenedensity \N \N \N \N \N \N \N \N \N \N \N
+151 2014-11-25 00:00:00 shortnoncodingdensity \N \N \N \N \N \N \N \N \N \N \N
+152 2014-11-25 00:00:00 codingdensity \N \N \N \N \N \N \N \N \N \N \N
+153 2014-11-25 00:00:00 percentagerepeat \N \N \N \N \N \N \N \N \N \N \N
+154 2014-05-09 15:05:36 ena_repeat ena \N \N \N \N \N \N \N \N ena_repeat repeat
+155 2014-05-09 15:05:36 ena_repeat_direct ena \N \N \N \N \N \N \N \N ena_repeat_direct repeat
+156 2014-12-02 00:00:00 snpdensity \N \N \N \N \N \N \N \N \N \N \N
+157 2014-07-17 17:46:20 go_projection GO \N \N GOProjection.pm \N \N \N \N \N \N \N
+183 2014-11-26 14:53:48 blastprodom ProDom 2006.1 \N blastprodom \N \N \N \N \N \N \N
+189 2014-11-26 14:53:58 pirsf PIRSF 2.84 \N pirsf \N \N \N \N \N \N \N
+185 2014-11-26 14:53:50 hamap HAMAP 201311.27 \N hamap \N \N \N \N \N \N \N
+192 2014-11-26 14:54:00 smart Smart 6.2 \N smart \N \N \N \N \N \N \N
+197 2014-11-26 14:54:04 tmhmm Tmhmm \N \N tmhmm \N \N \N \N \N \N \N
+184 2014-11-26 14:53:50 gene3d Gene3D 3.5.0 \N gene3d \N \N \N \N \N \N \N
+188 2014-11-26 14:53:57 pfscan Prosite_profiles 20.105 \N pfscan \N \N \N \N \N \N \N
+198 2014-11-26 14:54:05 seg Seg \N \N seg \N \N \N \N \N \N \N
+194 2014-11-26 14:54:02 tigrfam TIGRfam 13.0 \N tigrfam \N \N \N \N \N \N \N
+199 2014-11-26 14:54:06 interpro2go InterPro2GO \N \N interpro2go \N \N \N \N \N \N \N
+193 2014-11-26 14:54:02 superfamily Superfamily 1.75 \N superfamily \N \N \N \N \N \N \N
+176 2014-11-19 15:16:28 iwgsc \N \N \N \N \N \N \N \N \N \N \N
+182 2014-11-26 14:00:43 xrefuniparc \N \N \N \N \N \N \N \N \N \N \N
+180 2014-11-21 13:43:55 repeatmask repbase 20140131 /nfs/panda/ensemblgenomes/external/RepeatMasker/Libraries/RepeatMaskerLib.embl RepeatMasker 3.3.0 /nfs/panda/ensemblgenomes/external/bin/RepeatMasker -nolow -s -gccalc -species "Triticum aestivum" Bio::EnsEMBL::Analysis::Runnable::RepeatMasker \N repeatmasker repeat_region
+181 2014-11-23 19:32:29 repeatmask_trep custom \N /nfs/panda/ensemblgenomes/external/data/repeats_libraries/trep/trep.nr RepeatMasker 3.3.0 /nfs/panda/ensemblgenomes/external/bin/RepeatMasker -nolow -s -gccalc -lib "/nfs/panda/ensemblgenomes/external/data/repeats_libraries/trep/trep.nr" Bio::EnsEMBL::Analysis::Runnable::RepeatMasker \N repeatmasker repeat_region
diff --git a/modules/t/test-genome-DBs/polyploidy/core/analysis_description.txt b/modules/t/test-genome-DBs/polyploidy/core/analysis_description.txt
new file mode 100644
index 0000000000..7878e52347
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/analysis_description.txt
@@ -0,0 +1,48 @@
+178 <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/27/2/573?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Benson&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/1999&tdate=12/31/1999&resourcetype=HWCIT">Tandem Repeats Finder</a> locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N
+177 Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits. Low complexity (Dust) 1 \N
+101 <a href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a> alignments (coverage >=95%, %id >= 94%) of predicted ORFs assembled from <i>Triticum aestivum</i> (bread wheat) public datasets. Supplied by <a href="http://www.tgac.ac.uk">The Center for Genome Analysis</a> as part of the <a href="http://maswheat.ucdavis.edu/Transcriptome/">Triticeae-CAP</a> project. Published as supplemental dataset 7, in <a href="http://genomebiology.com/content/14/6/R66">Krasileva et al.</a>, PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23800085">23800085</a>. T. aestivum RNA-seq alignment 1 {'label_key' => '[biotype]', colour_key => '[biotype]', 'default' => {'MultiTop' => 'gene_label', 'contigviewbottom' => 'transcript_label', 'MultiBottom' => 'collapsed_label', 'contigviewtop' => 'gene_label', 'cytoview' => 'gene_label', 'alignsliceviewbottom' => 'as_collapsed_label' }, name => 'T. aestivum RNA-seq alignments', caption => 'T. aestivum RNA-seq alignments', multi_name => 'T. aestivum RNA-seq alignments'}
+186 HMM-Panther families PANTHER 1 {'type' => 'domain'}
+195 Prediction of coiled-coil regions in proteins is by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>. Coiled-coils (Ncoils) 1 \N
+184 Gene3D analysis as of interpro_scan.pl Gene3D 1 {'type' => 'domain'}
+188 Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome. PROSITE profiles 1 {'type' => 'domain'}
+198 Identification of peptide low complexity sequences by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFV-44PXMF3-45&_user=776054&_coverDate=06%2F30%2F1993&_rdoc=6&_fmt=high&_orig=browse&_srch=doc-info(%23toc%235236%231993%23999829997%23279143%23FLP%23display%23Volume)&_cdi=5236&_sort=d&_docanchor=&_ct=13&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=ac6f98882f2c6626643118367fb28cad">Seg</a>. Low complexity (Seg) 1 \N
+187 Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D138?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Bateman&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">Pfam</a> database. Pfam 1 {'type' => 'domain'}
+190 Protein fingerprints (groups of conserved motifs) are aligned to the genome. These motifs come from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/31/1/400?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Attwood&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">PRINTS</a> database. Prints 1 {'type' => 'domain'}
+183 NCBI-BlastP search against ProDom families ProDom 1 {'type' => 'domain'}
+189 Protein domains and motifs from the <a rel="external" href="http://pir.georgetown.edu/pirwww/index.shtml">PIR (Protein Information Resource)</a> Superfamily database. PIRSF 1 {'type' => 'domain'}
+185 HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins HAMAP 1 {'type' => 'domain'}
+192 Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D257?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=letunic&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2006&tdate=12/31/2006&resourcetype=HWCIT">SMART</a> database. SMART 1 {'type' => 'domain'}
+197 Prediction of transmembrane helices in proteins by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D7V9-K&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=a113464457fa5206c6699b9d464cbfee">TMHMM</a>. Transmembrane helices 1 \N
+191 Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome. PROSITE patterns 1 {'type' => 'domain'}
+196 Prediction of signal peptide cleavage sites by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_user=776054&_coverDate=07%2F16%2F2004&_alid=772330061&_rdoc=1&_fmt=high&_orig=search&_cdi=6899&_sort=d&_docanchor=&view=c&_ct=1&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=9f42be939814b7711268fd414604c9dd">SignalP</a>. Cleavage site (Signalp) 1 {'type' => 'feature'}
+200 InterPro2Pathway mapping is obtained from interproScan results. InterPro2Pathway mapping 1 \N
+194 Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/31/1/371?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Haft&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2003&tdate=12/31/2003&resourcetype=HWCIT">TIGRFAM</a> database. TIGRFAM 1 {'type' => 'domain'}
+119 <i>Triticum aestivum</i> genes annotated by <a href="http://mips.helmholtz-muenchen.de/plant/wheat/">MIPS</a> MIPS 1 {'colour_key' => '[biotype]', 'label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'}, 'name' => 'Protein-coding Gene (MIPS)', 'caption' => 'Protein-coding Gene (MIPS)', 'multi_name' => 'Protein-coding Gene (MIPS)','key' => 'ensembl'}
+45 <i>T. aestivum</i> Inter-homoeologous Variants that differ between the A and D genomes (where the B genome is unknown) Brenchley et al. T. aestivum Genome A/D SNPs 1 \N
+46 <i>T. aestivum</i> Inter-homoeologous Variants that are the same between the A and D genomes, but differ in B Brenchley et al. T. aestivum Genome B SNPs 1 \N
+136 Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or "Xrefs". DNA match 0 \N
+137 match Protein 0 \N
+138 Xref mapping based on checksum equivalency Xref checksum 0 \N
+100 <a href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a> alignments (coverage >=95%, %id >= 94%) of predicted ORFs assembled from <i>Triticum turgidum</i> (durum wheat) RNA-seq. Supplied by <a href="http://www.tgac.ac.uk">The Center for Genome Analysis</a> as part of the <a href="http://maswheat.ucdavis.edu/Transcriptome/">Triticeae-CAP</a> project. Published as supplemental dataset 7, in <a href="http://genomebiology.com/content/14/6/R66">Krasileva et al.</a>, PMID:<a href="http://www.ncbi.nlm.nih.gov/pubmed/23800085">23800085</a>. T. turgidum RNA-seq alignment 1 {'label_key' => '[biotype]', colour_key => '[biotype]', 'default' => {'MultiTop' => 'gene_label', 'contigviewbottom' => 'transcript_label', 'MultiBottom' => 'collapsed_label', 'contigviewtop' => 'gene_label', 'cytoview' => 'gene_label', 'alignsliceviewbottom' => 'as_collapsed_label' }, name => 'T. turgidum RNA-seq alignments', caption => 'T. turgidum RNA-seq alignments', multi_name => 'T. turgidum RNA-seq alignments)'}
+140 ncRNA genes are predicted using a combination of methods depending on their type. tRNAs are predicted using <a href="http://selab.janelia.org/tRNAscan-SE/">tRNAScan-SE</a>, rRNAs using <a href="http://www.cbs.dtu.dk/services/RNAmmer/">RNAmmer</a>, and for all other types, using covariance models and sequences from <a href="http://rfam.sanger.ac.uk/">RFAM</a>. ncRNA 1 {'colour_key' => '[biotype]','caption' => 'ncRNA','label_key' => '[biotype]','name' => 'ncRNA','default' => {'contigviewbottom' =>'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'},'key' => 'ncRNA'}
+141 Protein coding genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a> Protein coding genes (ENA) 1 {'colour_key' => '[biotype]','caption' => 'Genes','name' => 'Genes','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'multi_caption' => 'Genes','key' => 'ena_genes'}
+142 Cross-references attached by GenomeLoader GenomeLoader cross-references 1 \N
+143 Cross-references attached by GenomeLoader to provide names GenomeLoader name cross-references 1 \N
+145 ncRNA genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a> ncRNA genes (ENA) 1 {'colour_key' => '[biotype]','caption' => 'Genes','name' => 'Genes','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'multi_caption' => 'Genes','key' => 'ena_genes'}
+146 gene feature annotated in ENA gene (ENA) 1 {'multi_name' => 'Genomic features','caption' => 'Genomic features','name' => 'Genomic features','label_key' => '[text_label] [display_label]','key' => 'ena_features'}
+147 exon feature annotated in ENA exon (ENA) 1 {'multi_name' => 'Genomic features','caption' => 'Genomic features','name' => 'Genomic features','label_key' => '[text_label] [display_label]','key' => 'ena_features'}
+148 Percentage of G/C bases in the sequence. GC content 1 \N
+149 Long non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">LongNonCodingDensity.pm</a>. Long non-coding genes (density) 1 \N
+150 Pseudogene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/PseudogeneDensity.pm?root=ensembl&view=markup">PseudogeneDensity.pm</a>. Pseudogenes (density) 1 \N
+151 Short non-coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Production/Pipeline/Production/NonCodingDensity.pm?root=ensembl&view=markup">ShortNonCodingDensity.pm</a>. Short non-coding genes (density) 1 \N
+152 Coding gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/CodingDensity.pm?root=ensembl&view=markup">CodingDensity.pm</a>. Coding genes (density) 1 \N
+153 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N
+154 Repeat regions annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a> Repeats (ENA) 1 \N
+155 Direct repeat regions annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a> Direct repeats (ENA) 1 \N
+156 Density of single nucleotide polymorphisms (SNPs) as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm?root=ensembl&view=markup">SNPDensity.pm</a>. SNP Density 1 \N
+157 The XRef projection pipeline re-implemented by CK based on work by Andy and tweaked by Dan Projected XRef 0 \N
+199 InterPro2GO file is generated manually by the InterPro team at the EBI. InterPro2GO mapping 1 \N
+193 Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457CXWM-3D&_user=776054&_coverDate=11%2F02%2F2001&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=17&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=a921e84cd71c59f75644aa28f3224b58">SUPERFAMILY</a> database. Superfamily 1 {'type' => 'domain'}
+176 <i>Triticum aestivum</i> 3B chromosome genes annotated by <a href="http://www6.clermont.inra.fr/umr1095_eng">INRA GDEC group</a> GDEC 3B annotation 1 {'colour_key' => '[biotype]', 'label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'}, 'name' => 'GDEC', 'caption' => 'GDEC', 'multi_name' =>'GDEC','key' => 'gdec'}
+180 <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> is used to find repeats and low-complexity sequences. This track usually shows repeats alone (not low-complexity sequences). Repeats 1 \N
+181 Repeats detected using the <a href="http://wheat.pw.usda.gov/ITMI/Repeats/">TREP</a> library (trep.nr) using <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a>. Repeats TREP library 1 \N
diff --git a/modules/t/test-genome-DBs/polyploidy/core/assembly.txt b/modules/t/test-genome-DBs/polyploidy/core/assembly.txt
new file mode 100644
index 0000000000..408ed0fff5
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/assembly.txt
@@ -0,0 +1,3 @@
+3495644 3309354 1 4562 1 4562 1
+3495727 3355688 1 18301 1 18301 1
+3495794 3116582 1 5428 1 5428 1
diff --git a/modules/t/test-genome-DBs/polyploidy/core/assembly_exception.txt b/modules/t/test-genome-DBs/polyploidy/core/assembly_exception.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/associated_group.txt b/modules/t/test-genome-DBs/polyploidy/core/associated_group.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/associated_xref.txt b/modules/t/test-genome-DBs/polyploidy/core/associated_xref.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/attrib_type.txt b/modules/t/test-genome-DBs/polyploidy/core/attrib_type.txt
new file mode 100644
index 0000000000..d0def85500
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/attrib_type.txt
@@ -0,0 +1,296 @@
+1 embl_acc European Nucleotide Archive (was EMBL) accession \N
+2 status Status \N
+3 synonym Synonym \N
+4 name Name Alternative/long name
+5 type Type of feature \N
+6 toplevel Top Level Top Level Non-Redundant Sequence Region
+7 GeneCount Gene Count Total Number of Genes
+8 KnownGeneCount Known Gene Count Total Number of Known Genes
+9 PseudoGeneCount PseudoGene Count Total Number of PseudoGenes
+10 SNPCount Short Variants Total Number of SNPs
+11 codon_table Codon Table Alternate codon table
+12 _selenocysteine Selenocysteine \N
+13 bacend bacend \N
+14 htg htg High Throughput phase attribute
+15 miRNA Micro RNA Coordinates of the mature miRNA
+16 non_ref Non Reference Non Reference Sequence Region
+17 sanger_project Sanger Project name \N
+18 clone_name Clone name \N
+19 fish FISH location \N
+21 org Sequencing centre \N
+22 method Method \N
+23 superctg Super contig id \N
+24 inner_start Max start value \N
+25 inner_end Min end value \N
+26 state Current state of clone \N
+27 organisation Organisation sequencing clone \N
+28 seq_len Accession length \N
+29 fp_size FP size \N
+30 BACend_flag BAC end flags \N
+31 fpc_clone_id fpc clone \N
+32 KnwnPCCount protein_coding_KNOWN Number of Known Protein Coding
+33 NovPCCount protein_coding_NOVEL Number of Novel Protein Coding
+34 NovPTCount processed_transcript_NOVEL Number of Novel Processed Transcripts
+35 PutPTCount processed_transcript_PUTATIVE Number of Putative Processed Transcripts
+36 PredPCCount protein_coding_PREDICTED Number of Predicted Protein Coding
+37 IGGeneCount IG_gene Number of IG Genes
+38 IGPsGenCount IG_pseudogene Number of IG Pseudogenes
+39 TotPsCount total_pseudogene Total Number of Pseudogenes
+42 KnwnPCProgCount protein_coding_in_progress_KNOWN Number of Known Protein Coding in progress
+43 NovPCProgCount protein_coding_in_progress_NOVEL Number of Novel Protein Coding in progress
+44 AnnotSeqLength Annotated sequence length Annotated Sequence
+45 TotCloneNum Total number of clones Total Number of Clones
+46 NumAnnotClone Fully annotated clones Number of Fully Annotated Clones
+47 ack Acknowledgement Acknowledgement for manual annotation
+48 htg_phase High throughput phase High throughput genomic sequencing phase
+49 description Description A general descriptive text attribute
+50 chromosome Chromosome Chromosomal location for supercontigs that are not assembled
+51 nonsense Nonsense Mutation Strain specific nonesense mutation
+52 author Author Group resonsible for Vega annotation
+53 author_email Author email address Author email address
+54 remark Remark Annotation remark
+55 transcr_class Transcript class Transcript class
+56 KnwnPTCount processed_transcript_KNOWN Number of Known Processed Transcripts
+57 ccds CCDS CCDS identifier
+58 CCDS_PublicNote CCDS Public Note Public Note for CCDS identifier, provided by http://www.ncbi.nlm.nih.gov/CCDS
+59 Frameshift Frameshift Frameshift modelled as intron
+60 PTCount processed_transcript Number of Processed Transcripts
+61 PredPTCount processed_transcript_PREDICTED Number of Predicted Processed Transcripts
+62 ncRNA Structure RNA secondary structure line
+63 skip_clone skip clone Skip clone in align_by_clone_identity.pl \N
+64 coding_cnt Coding genes Number of protein coding Genes
+65 GeneNo_novCod novel protein_coding Gene Count Number of novel protein_coding Genes
+66 GeneNo_rRNA rRNA Gene Count Number of rRNA Genes
+67 pseudogene_cnt Pseudogenes Number of pseudogenes
+68 GeneNo_snRNA snRNA Gene Count Number of snRNA Genes
+69 GeneNo_snoRNA snoRNA Gene Count Number of snoRNA Genes
+70 GeneNo_miRNA miRNA Gene Count Number of miRNA Genes
+71 GeneNo_mscRNA misc_RNA Gene Count Number of misc_RNA Genes
+72 GeneNo_scRNA scRNA Gene Count Number of scRNA Genes
+73 GeneNo_MTrRNA Mt_rRNA Gene Count Number of Mt_rRNA Genes
+74 GeneNo_MTtRNA Mt_tRNA Gene Count Number of Mt_tRNA Genes
+75 GeneNo_RNA_pseu RNA_pseudogene Gene Count Number of RNA_pseudogene Genes
+76 GeneNo_tRNA tRNA Gene Count Number of tRNA Genes
+77 GeneNo_rettran retrotransposed Gene Count Number of retrotransposed Genes
+78 GeneNo_snlRNA snlRNA Gene Count Number of snlRNA Genes
+79 GeneNo_proc_tr processed_transcript Gene Count Number of processed transcript Genes
+80 supercontig SuperContig name \N
+81 well_name Well plate name \N
+82 bacterial Bacterial \N
+83 NovelCDSCount Novel CDS Count \N
+84 NovelTransCount Novel Transcript Count \N
+85 PutTransCount Putative Transcript Count \N
+86 PredTransCount Predicted Transcript Count \N
+87 UnclassPsCount Unclass Ps count \N
+88 KnwnprogCount Known prog Count \N
+89 NovCDSprogCount Novel CDS prog count \N
+90 bacend_well_nam BACend well name \N
+91 alt_well_name Alt well name \N
+92 TranscriptEdge Transcript Edge \N
+93 alt_embl_acc Alt European Nucleotide Archive (was EMBL) acc \N
+94 alt_org Alt org \N
+95 intl_clone_name International Clone Name \N
+96 embl_version European Nucleotide Archive (was EMBL) Version \N
+97 chr Chromosome Name Chromosome Name Contained in the Assembly
+98 equiv_asm Equivalent EnsEMBL assembly For full chromosomes made from NCBI AGPs
+99 GeneNo_ncRNA ncRNA Gene Count Number of ncRNA Genes
+100 GeneNo_Ig Ig Gene Count Number of Ig Genes
+109 HitSimilarity hit similarity percentage id to parent transcripts
+110 HitCoverage hit coverage coverage of parent transcripts
+111 PropNonGap proportion non gap proportion non gap
+112 NumStops number of stops \N
+113 GapExons gap exons number of gap exons
+114 SourceTran source transcript source transcript
+115 EndNotFound end not found end not found
+116 StartNotFound start not found start not found
+117 Frameshift Fra Frameshift modelled as intron \N
+118 ensembl_name Ensembl name Name of equivalent Ensembl chromosome
+119 NoAnnotation NoAnnotation Clones without manual annotation
+120 hap_contig Haplotype contig Contig present on a haplotype
+121 annotated Clone Annotation Status \N
+122 keyword Clone Keyword \N
+123 hidden_remark Hidden Remark \N
+124 mRNA_start_NF mRNA start not found \N
+125 mRNA_end_NF mRNA end not found \N
+126 cds_start_NF CDS start not found \N
+127 cds_end_NF CDS end not found \N
+128 write_access Write access for Sequence Set 1 for writable , 0 for read-only
+129 hidden Hidden Sequence Set \N
+130 vega_name Vega name Vega seq_region.name
+131 vega_export_mod Export mode E (External), I (Internal) etc
+132 vega_release Vega release Vega release number
+133 atag_CLE Clone_left_end Clone_lef_end feature marked in GAP database
+134 atag_CRE Clone_right_end Clone_right_end feature marked in GAP database
+135 atag_Misc Misc miscellaneous feature marked in GAP database
+136 atag_Unsure Unsure region of uncertain DNA sequence marked in GAP database
+137 MultAssem Multiple Assembled seq region Part of Seq Region is part of more than one assembly
+140 wgs WGS contig WGS contig integrated into the map
+141 bac AGP clones tiling path of clones
+142 GeneGC Gene GC Percentage GC content for this gene
+143 TotAssemblyLeng Finished sequence length Length of the assembly not counting sequence gaps
+144 amino_acid_sub Amino acid substitution Some translations have been manually curated for amino acid substitiutions. For example a stop codon may be changed to an amino acid in order to prevent premature truncation, or one amino acid can be substituted for another.
+145 _rna_edit rna_edit RNA edit
+146 kill_reason Kill Reason Reason why a transcript has been killed
+147 strip_UTR Strip UTR Transcript needs bad UTR removing
+148 TotAssLength Finished sequence length Finished Sequence
+149 PsCount pseudogene Number of Pseudogenes
+152 TotPTCount total_processed_transcript Total Number of Processed Transcripts
+153 TotPCCount total_protein_coding Total Number of Protein Coding
+154 NovNcCount novel_non_coding Number of Novel Non Coding
+155 KnwnPolyPsCount known_polymorphic Number of Known Polymorphic Pseudogenes
+156 PolyPsCount polymorphic_pseudogene Number of Polymorphic Pseudogenes
+157 TotIGGeneCount total_IG_gene Total Number of IG Genes
+158 ProcPsCount proc_pseudogene Number of Processed Pseudogenes
+159 UnPsCount unproc_pseudogene Number of Unprocessed Pseudogenes
+160 TPsCount transcribed_pseudogene Number of Transcribed Pseudogenes
+161 TECCount TEC Number of TEC Genes
+162 KnwnIGGeneCount IG_gene_KNOWN Number of Known IG Genes
+163 KnwnIGPsGeCount IG_pseudogene_KNOWN Number of Known IG Pseudogenes
+164 IsoPoint Isoelectric point Pepstats attributes
+165 Charge Charge Pepstats attributes
+166 MolecularWeight Molecular weight Pepstats attributes
+167 NumResidues Number of residues Pepstats attributes
+168 AvgResWeight Ave. residue weight Pepstats attributes
+170 initial_met Initial methionine Set first amino acid to methionine
+171 NonGapHCov NonGapHCov \N
+172 otter_support otter support Evidence ID that was used as supporting feature for building a gene in Vega
+173 enst_link enst link Code to link a OTTT with an ENST when they both share the CDS of ENST
+174 upstream_ATG upstream ATG Alternative ATG found upstream of the defined as start ATG for the transcript
+175 TPPsCount transcribed_processed_pseudogene Number of Transcribed Processed Pseudogenes
+176 TUPsCount transcribed_unprocessed_pseudogene Number of Transcribed Unprocessed Pseudogenes
+177 UniPsCount unitary_pseudogene Number of Unitary Pseudogenes
+178 KnwnTECCount TEC_KNOWN Number of Known TEC genes
+179 TotTECGeneCount TEC_all Total number of TEC genes
+180 TUyPsCount transcribed_unitary_pseudogene Number of Transcribed Unitary Pseudogenes
+181 PolyCount polymorphic Number of Polymorphic Genes
+182 KnwnPolyCount polymorphic Number of Known Polymorphic Genes
+183 KnwnTRCount TR_gene_known Number of Known TR Genes
+184 TRGeneCount TR_gene Number of TR Genes
+185 TRPsCount TR_pseudo Number of TR Pseudogenes
+186 tp_ott_support otter protein transcript support Evidence ID that was used as supporting feature for building a gene in Vega
+187 td_ott_support otter dna transcript support Evidence ID that was used as supporting feature for building a gene in Vega
+188 ep_ott_support otter protein exon support Evidence ID that was used as supporting feature for building a gene in Vega
+189 ed_ott_support otter dna exon support Evidence ID that was used as supporting feature for building a gene in Vega
+190 GeneNo_lincRNA lincRNA Gene Count Number of lincRNA Genes
+191 StopGained SNP causes stop codon to be gained This transcript has a variant that causes a stop codon to be gained in at least 10 percent of a HapMap population
+192 StopLost SNP causes stop codon to be lost This transcript has a variant that causes a stop codon to be lost in at least 10 percent of a HapMap population
+193 GeneNo_class_I_ class_I_RNA Gene Count Number of class_I_RNA Genes
+194 GeneNo_SRP_RNA SRP_RNA Gene Count Number of SRP_RNA Genes
+195 GeneNo_class_II class_II_RNA Gene Count Number of class_II_RNA Genes
+196 GeneNo_P_RNA RNase_P_RNA Gene Count Number of RNase_P_RNA Genes
+197 GeneNo_RNase_MR RNase_MRP_RNA Gene Count Number of RNase_MRP_RNA Genes
+198 lost_frameshift lost_frameshift Frameshift on the query sequence is lost in the target sequence
+199 AltThreePrime Alternate three prime end The position of other possible three prime ends for the transcript
+216 GeneInLRG Gene in LRG This gene is contained within an LRG region
+217 GeneOverlapLRG Gene overlaps LRG This gene is partially overlapped by a LRG region (start or end outside LRG)
+218 readthrough_tra readthrough transcript Havana readthrough transcripts
+300 CNE Constitutive exon An exon that is always included in the mature mRNA, even in different mRNA isoforms
+301 CE Cassette exon One exon is spliced out of the primary transcript together with its flanking introns
+302 IR Intron retention A sequence is spliced out as an intron or remains in the mature mRNA transcript
+303 MXE Mutually exclusive exons In the simpliest case, one or two consecutive exons are retained but not both
+304 A3SS Alternative 3' sites Two or more splice sites are recognized at the 5' end of an exon. An alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon
+305 A5SS Alternative 5' sites Two or more splice sites are recognized at the 3' end of an exon. An alternative 5' splice junction (donor site) is used, changing the 3' boundary of the upstream exon
+306 AFE Alternative first exon The second exons of each variant have identical boundaries, but the first exons do not overlap
+307 ALE Alternative last exon Penultimate exons of each splice variant have identical boundaries, but the last exons do not overlap
+308 II Intron isoform Alternative donor or acceptor splice sites lead to truncation or extension of introns, respectively
+309 EI Exon isoform Alternative donor or acceptor splice sites leads to truncation or extension of exons, respectively
+310 AI Alternative initiation Alternative choice of promoters
+311 AT Alternative termination Alternative choice of polyadenylation sites
+312 patch_fix Assembly Patch Fix Assembly patch that will, in the next assembly release, replace the corresponding sequence found in the current assembly
+313 patch_novel Assembly Patch Novel Assembly patch that will, in the next assembly release, be retained as an alternate non-reference sequence in a similar way to haplotypes
+314 LRG Locus Reference Genomic Locus Reference Genomic sequence
+315 NoEvidence Evidence for transcript removed Supporting evidence for this projected transcript has been removed
+316 circular_seq Circular sequence Circular chromosome or plasmid molecule
+317 external_db External database External database to which seq_region name may be linked
+318 split_tscript split_tscript split_tscript
+319 Threep Three prime end Alternate three prime end
+320 gene_cluster Gene cluster Havana annotated gene cluster
+328 _rib_frameshift Ribosomal Frameshift Position and magnitude of frameshift
+345 vega_ref_chrom Vega reference chromosome Haplotypes reference a regular chromosome (indicated in the value of the attribute)
+346 PutPCCount protein_coding_PUTATIVE Number of Putative Protein Coding
+347 proj_alt_seq Projection altered sequence Projected sequence differs from original
+348 hav_gene_type Havana gene biotype Gene biotype assigned by Havana
+349 GeneNo_asense antisense Gene Count Number of antisense Genes
+350 GeneNo_sense_in sense_intronic Gene Count Number of sense_intronic Genes
+351 GeneNo_amb_orf ambiguous_orf Gene Count Number of ambiguous_orf Genes
+352 GeneNo_ret_int retained_intron Gene Count Number of retained_intron Genes
+353 noncoding_cnt Non coding gene count Number of non coding genes
+354 GeneNo_ncrna_h ncrna_host Gene Count Number of ncrna_host Genes
+355 GeneNo_sens_ov sense_overlapping Gene Count Number of sense_overlapping Genes
+356 GeneNo_3prime 3prime_overlapping Gene Count Number of 3prime_overlapping Genes
+357 GeneNo_tmRNA tmRNA Gene Count Number of tmRNA Genes
+358 PHIbase_mutant PHI-base mutant PHI-base phenotype of the mutants
+359 GeneNo_ribozyme ribozyme Gene Count Number of ribozyme Genes
+360 ncrna_host ncrna_host Havana ncrna_host gene
+361 peptide-class Peptide classification The classification of the gene or transcript based on alignment to NR (values: TE WH NH)
+362 working-set Working Gene Set High-confidence set of genes, composed of evidence-based genes and non-overlapping protein-coding ab initio gene models
+363 filtered-set Filtered Gene Set v1 Working genes that are screened for TE content and orthology with sorghum and rice.
+364 super-set Super Working Gene Set Set of all working gene set loci from both Builds 4a and 5a
+365 projected4a2 Projected by alignment Temporary (Monday, August 23, 2010)
+366 merged Merged species \N
+367 karyotype_rank Rank in the karyotype For a given seq_region, if it is part of the species karyotype, will indicate its rank
+368 noncoding_acnt Alternate non coding gene count Number of non coding genes on alternate sequences
+369 coding_acnt Coding genes Number of protein coding genes on alternate sequences
+370 pseudogene_acnt Pseudogenes Number of pseudogenes on alternate sequences
+371 clone_end Clone end Side of the contig on which a vector lies (enum:RIGHT, LEFT).
+372 contig_scaffold Contig Scaffold Scaffold that contains mutually ordered contigs.
+373 current_version Current Accession Version Identifies the most recent version of an accession.
+374 seq_status Sequence Status Sequence status.
+375 clone_vector Vector sequence A clone-end vector associated with a contig (enum:SP6, T7).
+376 creation_date Creation date Creation date of annotation
+377 update_date Update date Last update date of annotation
+378 seq_date Sequence date Sequence date
+379 has_stop_codon Contains stop codon Translation attribute
+380 havana_cv Havana CV term Controlled vocabulary terms from Havana
+381 TlPPsCount translated_processed_pseudogene Number of Translated Processed Pseudogenes
+382 NoTransRefError No translations due to reference error This gene is believed to include protein coding transcripts, but no transcript has a translation due to a reference assembly error making specifying the translation impossible.
+383 parent_exon_key parent_exon_key The exon key to identify a projected transcript's parent transcript.
+386 parent_sid parent_sid The parent stable ID to identify a projected transcript's parent transcript. For internal statistics use only since this method does not work in all cases.
+387 snoncoding_acnt Small non coding genes Number of small non coding genes on alternate sequences
+388 lnoncoding_acnt Long non coding genes Number of long non coding genes on alternate sequences
+389 snoncoding_cnt Small non coding genes Number of small non coding genes
+390 lnoncoding_cnt Long non coding genes Number of long non coding genes
+391 TlUPsCount translated_unprocessed_pseudogene Number of Translated Unprocessed Pseudogenes
+393 AFFYMETRIXCount AFFYMETRIX Count Total Number of AFFYMETRIX features
+394 RFLPCount RFLP Count Total Number of RFLP features
+395 xref_id Xref ID ID of associated database reference
+396 vega_chr_type Vega chrom type Type of chromosome - haplotype, other, etc
+397 GeneNo_MRP_RNA MRP_RNA Gene Count Number of MRP_RNA Genes
+398 genscan Genscan gene predictions Number of prediction genes generated by Genscan
+399 gsc GSC gene prediction Number of prediction genes generated by gsc
+400 snap Snap gene prediction Number of prediction genes generated by Snap
+401 fgenesh FGENESH gene prediction Number of prediction genes generated by FGENESH
+402 genefinder Genefinder gene prediction Number of prediction genes generated by Genefinder
+403 transcript_cnt Gene transcripts Number of transcripts
+404 transcript_acnt Gene transcripts Number of transcripts on the alternate sequences
+405 ref_length Golden Path Length Length of the primary assembly
+406 total_length Base Pairs Total length of the assembly
+407 refseq_compare refseq_compare This attribute can be applied to both gene and transcript. It is supposed to give an indication of whether the annotation in the ensembl database is matched by annotation that we have imported from refseq. At the gene level, the match is unlikely to be an exact match because all or some of the transcripts may differ. Also, the biotype e.g. coding potential may differ. therefore, matching is a bit fuzzy and is done primarily on genomic location and then also takes gene length and gene name into consideration.
+408 coding_rcnt Readthrough coding genes Number of readthrough coding genes
+409 coding_racnt Readthrough coding genes Number of readthrough coding genes on alternate sequences
+410 lnoncoding_racnt Readthrough long non coding genes Number of readthrough long non coding genes on alternate sequences
+411 snoncoding_racnt Readthrough small non coding genes Number of readthrough small non coding genes on alternate sequences
+412 snoncoding_rcnt Readthrough small non coding genes Number of readthrough small non coding genes
+413 lnoncoding_rcnt Readthrough long non coding genes Number of readthrough long non coding genes
+414 pseudogene_rcnt Readthrough pseudogenes Number of readthrough pseudogenes
+415 pseudogene_racnt Readthrough pseudogenes Number of readthrough pseudogenes on alternate sequences
+416 gencode_level GENCODE annotation level level 1 (verified loci), level 2 (manually annotated loci), level 3 (automatically annotated loci)
+417 gencode_basic GENCODE basic annotation GENCODE Basic is a view provided by UCSC for users. It includes a subset of the GENCODE transcripts. In general, for protein coding genes it will show only the full length models (unless a protein coding genes has no full-length models, in which case other rules apply). For noncoding genes, it will also only show the full-length (mRNA start and end found) models (unless there are no full-length models, in which case other rules apply).
+418 struct_var Structural variants Total Number of structural variants
+419 genblast GenBlastG gene predictions Number of prediction genes generated by GenBlastG
+420 syn_gene_pairs Syntenic gene pairs Syntenic gene relationship from Gramene pipeline
+421 vectorbase_adar VectorBase gene predictions Number of prediction genes generated with MAKER, by VectorBase.
+422 trnascan tRNAscan-SE predictions Number of predicted tRNA genes generated by tRNAscan-SE
+423 tgac_pred_supp7 T. turgidum RNA-seq alignments Number of T. turgidum RNA-seq alignments from Krasileva et al.
+424 tgac_pred_supp17 T. aestivum RNA-seq alignments Number of T. aestivum RNA-seq alignments from Krasileva et al.
+425 genome_component Genome Component Name For polyploid genome, the genome component name the seq_region belongs to.
+426 transcript_whl RNA-seq transcripts RNA-seq transcripts from EchinoBase
+428 TSL Transcript Support Level Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure and data are provided by UCSC. The following categories are assigned to each of the evaluated annotations. tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA. tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs. tsl3 - the only support is from a single EST. tsl4 - the best supporting EST is flagged as suspect. tsl5 - no single transcript supports the model structure. tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes.Human leukocyte antigen (HLA) transcript. Immunoglobin gene transcript. T-cell receptor transcript. Single-exon transcript (will be included in a future version)
+429 protein_coverage Protein Coverage Protein coverage for this gene derived from geneTree in compara
+430 consensus_coverage Consensus Coverage Consensus coverage for this gene derived from geneTree in compara
+431 has_start_codon Contains start codon Translation attribute
+432 appris_pi APPRIS principal isoform Transcript expected to code for the main functional isoform based on a range of protein features. APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. http://appris.bioinfo.cnio.es/ http://nar.oxfordjournals.org/content/41/D1/D110.long. Icon is {APPRIS} in green.
+433 appris_ci APPRIS candidate principal isoform APPRIS candidate principal isoform: Where there is no single 'appris_principal' variant the main functional isoform will be translated from one of the 'appris_candidate' genes. APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. http://appris.bioinfo.cnio.es/ http://nar.oxfordjournals.org/content/41/D1/D110.long. Icon is {APPRIS} in amber.
+434 appris_ci1 APPRIS candidate principal isoform (longest coding sequence) APPRIS candidate principal isoform (longest coding sequence): Where there is no single 'appris_principal' variant the main functional isoform will be translated from one of the 'appris_candidate' genes. Where there is no 'appris_candidate_ccd' or 'appris_candidate_longest_ccds' variant, the longest protein of the 'appris_candidate' variants is selected as the primary variant. APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. http://appris.bioinfo.cnio.es/ http://nar.oxfordjournals.org/content/41/D1/D110.long. Icon is {APPRIS*} in amber.
+435 appris_ci2 APPRIS candidate principal isoform (longest CCDS) APPRIS candidate principal isoform (longest CCDS): Where there is no single 'appris_principal' variant the main functional isoform will be translated from one of the 'appris_candidate' genes. When there are several 'appris_candidate' transcripts in CCDS, APPRIS labels the longest CCDS. APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. http://appris.bioinfo.cnio.es/ http://nar.oxfordjournals.org/content/41/D1/D110.long. Icon is {APPRIS**} in amber.
+436 appris_ci3 APPRIS candidate principal isoform (CCDS) APPRIS candidate principal isoform (CCDS): Where there is no single 'appris_principal' variant the main functional isoform will be translated from one of the 'appris_candidate' genes. This 'appris_candidate' transcript is unique in being part of CCDS. APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. http://appris.bioinfo.cnio.es/ http://nar.oxfordjournals.org/content/41/D1/D110.long. Icon is {APPRIS***} in amber.
diff --git a/modules/t/test-genome-DBs/polyploidy/core/coord_system.txt b/modules/t/test-genome-DBs/polyploidy/core/coord_system.txt
new file mode 100644
index 0000000000..6165106625
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/coord_system.txt
@@ -0,0 +1,4 @@
+10 1 scaffold IWGSP1 4 \N
+7 1 contig \N 3 default_version,sequence_level
+8 1 scaffold IWGSC2 2 default_version
+9 1 chromosome IWGSC2 1 default_version
diff --git a/modules/t/test-genome-DBs/polyploidy/core/data_file.txt b/modules/t/test-genome-DBs/polyploidy/core/data_file.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/density_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/density_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/density_type.txt b/modules/t/test-genome-DBs/polyploidy/core/density_type.txt
new file mode 100644
index 0000000000..2e10be4282
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/density_type.txt
@@ -0,0 +1,7 @@
+22 156 0 150 sum
+8 149 0 150 sum
+21 150 0 150 sum
+16 151 0 150 sum
+20 153 0 150 ratio
+19 152 0 150 sum
+17 148 0 150 ratio
diff --git a/modules/t/test-genome-DBs/polyploidy/core/dependent_xref.txt b/modules/t/test-genome-DBs/polyploidy/core/dependent_xref.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/ditag.txt b/modules/t/test-genome-DBs/polyploidy/core/ditag.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/ditag_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/ditag_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/dna.txt b/modules/t/test-genome-DBs/polyploidy/core/dna.txt
new file mode 100644
index 0000000000..c32900cedb
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/dna.txt
@@ -0,0 +1,3 @@
+3116582 ATCCCATGTGGAGATACCAGACTGAACTAAGCGGTGGTTAAGCCCACAAAAGTCCATAATTATTTCAGCTTTGTGCTTGATGAACCATCCCCAGGCCCATCCACCACTTCACCAATCTAACAATTTCATTTATGAAAAGATAAGTCACAGCTGAATTCAAAGTAACAACTATACAAAGAACAATGCCACAGCCAGGTCAGGCATGGTAAAAGTATATCGAGTGCTAAATGAGGTTTCATTTTATGTGTAACAAATACTCCCTCCGTCCGAAAATACTTGTCATCAAAATGGACAAAAAGGAACGTATCTAGAACTAAAATACATCTAGATACATCCCTTTTTATTCATTTTGATGACAAGTATTTCCGGACGGAGGGAGTATGTGTCATGAACCCTATCATATTCGAAGATTGTATGTGTGAATTTGAACCATTACTGTGGGCATGCAGTGATGCCTCACGGGTACCTCAAATTGCATAACAACTTGCATATAGGTTAAATAACTCAATCAGCATCAAGCAGTTACAAAAAGCAACACACTAATATCCTCAGCTTTGCTGATTCTTTGATGTAACAACTTAATATAATACTCTGGAAAGGTCTAATGTACAAAGGTACTTACTTTGTCCCATTTTAGCTCTTTTGAATTCCATGAATAAGCAACACCGGTGTGTCCCTCTCTAACAATTAGCGTTTGTGCAACGATTCCTGCTTAGAGGGGGAAAAGGTTACAAACATTGCACTACTGTGCAAAAATAACACGCACGGCAATGACTAGATATTGTCACAGTTACTTTACATACACAAGTCCACGACACTAAAGAATTTAGAGAAAAAATGTTTTTATATTGTTATCTCCTTGACGAAGGAAGGTTTATTGGAAACTAGAAAGATATGAATATTTTCAAAAGCTCGAAATTATTTCAGTGTGCAATAGTGCATCTTCAATCCGATTTTAATTTTCAGCTCCATAATAAGCTGACCTGCAAAATTCACTACAAATAGTTGGAGCATCATGGAATCAACACAATACACGTGTACCGCATCAGAAAAATGAGATTTATGACCTTGTTGTGTCATTCCCGCAGCTCCTGATGGATCCATCAGCTTCAGTCCACCAACAGTCTTTCTGTAGAGAAAAAAATAGGCATAAATATAATTTGATTAACACCATGATTCCGGCTTTTTTTTGGACAAGAAAAAGTGTCGCCTAAAAATTAAGAAGTTAAAATAACAATTACAGGAGTAATCTGACAACAAAACTGATCCTTTAAGCAGAAGATGTTAAAACCTCAGAAATATGAAAAAAGAAAATCAGGAACCAACCTATATGCTGCAAGTTCCTCATCACGGCAGGGCCTATTATTGCCAGTTGTCCATATCCTCACAATTCCATCACAACATGCAGTTACAACATCGCCATTATCCAAAAATTTAGCATCCCATATACGGCCTGGGTGTTCAATGCTCTGAACACAGATTCCATCTGCATTATATTACTTACAGTCATATAACCAGGTACATGAAGAAAATTCTGCATTCTGCTACGTACTAACAACCAAAACCAAAAAACTGCAATGTACTGCACCTCCAATATAATTTTCATTTCTACAATGGTTCATATTATGAATCCAAACATACTATCCCAAAAAACAAGACAGATATATCCTAGCTGCATCCATGAAACACACAAATCAAATCAGCAGCCCAAGAACAAGCACGGCTTTACATCATAGATACAAGCGTAAAAGAAGGCGGGTAGTGTGGGTATTGAGATTCTTATTTTCAATATGGAAGAAAAGAAGACTCGAACTGCTCATGGACTAGCCAAAGGAGGAATCAGCAATACAGATGCTTAACGACAACCAGCAGATCTCTTTTTACTGATTGTCACAGTTTCCATTATATTGCTAAATACGAACTACCTTTCCCATATGCCACTGCCCAATATGTTTGATGTCAACGTATTTACAATCTTTTGCCTATAATGGAATCCCGTGCAATATTTTGCCTGTAACAGAATCCCACTTAACAGGAAGTACTATCATAGACTGGATTATTTTTGTTTGGAGAAAACATTAGACAGAGGCATAGGGAGACAAACCATCTGAGGAATCGATAGCAACCCCAATGGAACGGTCAGGGTTTAAAGAGTCATTCAGTACAGATGTCAATAAAAAAAAGCAAAAAACAAACCCAAACAAAGACAAGAGAAATATATAATGTTAAATCAGCTTGGGTCCATAGATCAGTTGTCACATATAGAAAACCGAATTAATATCAGTCAGTTCGGTTTTAGGTTCAGGTTAACAAAATGCACTGAAAGAACCGGCTCGTCCTATGGCCCCATTTCCTAGGGCCATGCTACCATCCTTATAGCTTAGCAAAAAAAAACAAGTACATCAAAATCTCAACTAAAGCCCGGCATGATCTCCACCAAGTCAGCTAGGCGCCTAGGCCCATCTCTTGCTCTCTCGTACCAATGCAATCACGACAGGCCACAGGGAAACAAAGTTACCAGCCGACATGCGTGCAATCCATCCCGACAACCAACAGCACTGCCCTCGGCAGGCCCATCAGCGGACTAGCACTCCTGCCAGTCTGTCACCATCAACAAGACGATTCAAAGGATTCAAAGAGAAGCAGCGCCATGTTGATTCAACAAGATTCTGGATTTCAATCATGGTCTGTTGACAAGATTCAAGTATTTGACAGCATGCGCACCCTGTTCTGCTATTGAATTACCTGCTAACATTACATTTTGGTTTAAACCGAAAAGCAAGCCGGAGTTTGGGTGAACCCAACTTCCGGTTTGTAGAACTTTCCAGGCTAGCTCGGTTGTCAATTTTAGTAAACCGAAATACCAAAAAAAGAGGAAGAACGAATGCCTACACCTAGATTAAAGTATAAAAAGAAATTATATCCTATAAACAAGTGCCACTGCATTTTAACAAGAATTCTCTAAAGCATACAAAATAAATCACCTTTCCATATCTTGACCGAGCGATCTCGACTGCCACTAGCAATAAGACCAGATGAATGAGCATCCACAGAATATACAAGAGAGGTATGGCCAATCATCTCCAACAGGGGTTGGCCAGTTAATGCCCATAACTTTATAGTTCTGCGACAAAACAAAATATTATATGTGATCATGTAAATGAGTAGCTGTAAACTGAAAGAATAAATTTGATGCACAAAAAATGTAAGACGATAATGAAAATGATGAAAAGCCAAATAGATGAGCATTTTATTTCAGCAAACCACTGGCAGGATATTAGTACGAATATCCAAGATTAAACGAGAAATTTTGATATCTTCATTTACAATTTTAGAACAAATAATAGCAGCTTCTACTATACTGCACCATCCTTTCGTTCAAAAGCAAGTGGAAATAGTCAAGTGATAACTTACCCATCATGTGATGCAGAGAGTATACCCATTCCTGGCATCTGTGCTAAACAACAAACAGTGTCTGCAATGGAACAACATTCTGTCAACCGATCAAGTATGTGTGGATGAGCACAACAAAAGTCAAAAGCACCAGTGCACATCAGGAGTTAACAAATAACCTGCATGCCCAGAGAATGTATGTAGACAAATCCTTCCTTTCCAAAGTTTGATGGTGGAATCACTTGAACCTATACAAAAGGGGAAAGGTGTAAAGTATTAATCAACCATTTGACAAGTACTCCCTCCGTAAAGAAATATAAGAGCATTTAGATCACTAAAGCAGTGATCCAAACACTCTTATATTTCTTTACAGAGGTAGTAATAGATATCCAAGGACAGTCATAATTGCTCTCGAATATACTTCCCGTAAAGTAATAGATATACAAAGCGGAAGCTCTACCCGTAAATAGTTCTCCCGAGGGCAGCTTAAGAACAGTTTGCACTGCGGCTTCATGGGCCACCAAGATCTCTACAGCATTGCCATCTCTCCACCTTCTCAAAGTACTGTGCATAATACAAGTGTCAGGGTACAGCAAGGAACCATCAGATACAATGGGGAAACTTCATAATTTATTAGCCCAATATGTCATCACATGCCCAAAACACCAAATACGCCGCAGCCTTAAACACAAGTAGCATTGGAAACCTTTTCTAACAGGGGACTCAGAGTGTAGAAAGAAACAGAAGTACAATATGTGCATTTGTACAAAAAAAATATAAGAAATATAAATTATCAAAGAAGGTACTGAATTTATGCATATTAGTACAAAGTTAGTACAAAGTTGAGTAACTTACTTTGGGACAGAGGGAGTATATTACATTCATGTTACATCACCACATCTGCCAAACAACTACCCCATGAACAAATTGTCTGCATTTGCAGTGTGATTACATCATATACAAGAAAGACCCTCAGGATGAAATCAGCACAAGCAAGCAATCAACAAGAAGTACGTGAGCAAGTTCTGCACAGGAATTACACTGGTTGGGAAAAAACATACCAGTCCATCGATGAAGATATAATGTCACCGTTGTCATCGATAGCAAGACCAGTCACCTGTGAGGTGTGACCCTTCATTGTTCCAACAACTTCTCCTGTATGCAAATTCCACAGCAATACTAGTGTATCCATGCCACCAGAAACAATTGCTCCTTCCGGAAAGCGATCAGAAGGAGGGGCCCAAACCATTGCACCAACAAAACTAAAATGTCCTGCAAGGGTTTTCGAGAGGACATATTCGCACTTCTTTTCCGGGTGCTGCGTCCAGAATCTCACGGTTCCATCGCTTGATGAGGTTGCAACACCCACATCACCACAGATACATATCCTAGAAACCTATTGTAAAAAGAGCAAGGACAAGTTAGCAAAGAATCAAATGTGCAGCAAATGTAGCAATTATGAAAGAGCTTGATTATAAGGATCTAACTTTATTGGTTGAATACATGCCAGTACTCAAAGTCTAAAACTACTTACTGATGTAGATATGCGTTCCACATATGCAAAATAACCTTTGCCTAAGCTCTTAACAGTTTGAGCAGAATAATCGGTTAATACACGGGGATCACCTTTATCTCCAAATTTGGTTGATCATCATATAAGCACTTCTTTATTTTCAACACTAACATGTTTCTCTTTTACTATCCTTTGGACAGACATGGGCTTGCATAAAGGGGTATTTGGTATTTACATGCTAAATGCAGGTTATAATTTGAACCATAAGTCCATCGTTAGAAAAACAGAACGTGGCATTCTGGATGAGCATGGATTCCTCAAATAAGCACAACAATTTGTTGAGTTTCTGGTGGAACATAACAGGGAAGTTACAATCTGATTACAAGTGTAAAAATAACTCAAGCAAAACCAAGTAACTGATCATTGCTTGATCCACAAATCCACTACAAATATAATATCAAAAGGAAGTCAAACTGCAATGACTAATCGCGCCAGATCCACGCCGCCCCGACCAAGGCCGCC
+3309354 GGCGCGATGTCGTGGAGTTCAGGGGCTTCTTCCGCTCCCGGATTCCGCCGCGCCAGTGGAAGGAGGGAGACGGACTCGAGGTCTCCTGTAGCTTACAGGGAGAGCCCAATGGCGTACGAGCCGCCGAAGATGTGCCATTGCAGACAGCCGCGCAAGGCGCCAAGATGGATCTCGTGGAGCCGCCAAAACCTTGGCAGGAGGTACTACGCCTGTGTGGATGCAATGGTGAGCCCCATTTTCTGTGTTTCTGCTGCTCTTTTCTTGCTCTTAGTTTGTGATTGATTTCATTTTCTGTTGAATAGCATGGTGGATGTGGCTATGTGGAATGGCATGATGATCCTTTGCCCACGTTTTTTAGCAACTTGATTGGAGATTTGAGAGACGAGGTGTGGAGGCTAAAGGGTCAGAGATCTGTGGCTGAGGCTGAAGATGGAATTCCAATTGTGCCTGTGTCTGGTCATGAAGCAGCATTACAGAATGTGGTTATGTCTCTGCAGGTTTAGTTAAAGGAGAAGAATGCAGAACTAGAAGCAATGAAAGGCAAATATATGAATGTGGTGATGGTTTTCATTGCCTTTGTGGTAGGTGTTTTCCTAGGGAAAGTGCTAGTGTTCTGAATGTGAGGTTAGCAGTTGGCATGAGTTATTTTGGTAGGAAAAAGTGCAAGTGCAATGAACATGTATGCAATGGTTTGTAATGCTATTATTTGTGATCTGGGAGTGGTTTGTTATCAATGAGACTATGATCTGGCAGTTAATAAAAATCTCAGTTTTAATGGAAGTTGCAGTAGCTATTTTGTATCAATTCTATGGAAATGAGCAAGTTGACTGTATGAGAACTCTGCTGTGAATATTGCTTGCATTTTGACAGCATTTCTGCTGGCATTTGCAGAATGTGCATATATATAGCAAAATGACAGTAATTGATTTGTAAGAAACAAAATGCAAACACAGTGCACATAAAGCAAACATTGCTTGAAATTTGACTGCATTTCGGTTGATAGCATCTCAGTTTACAACATCCCAGTTCACCAAAAGGACATACTTCATTAGAGGATCACCAAAAGCACATAGTTCAGTACATGATAACCAAAAGGACATAGTCCAGTACATGAGCAACACAAATATGTAACTAGTTGCCACTTGCAGTGAAGTATTGGTAGCTGGGCAGTGAAGATGCAGGAGCCCTCTTTCTTCTTTTATTTGTAGTAGATGGTCCAGCTTGTGCATTTGCTGATGACTTCTTGGGAGGTTTAAACCTTGAAGTTGCAGTACTTGGCACAGTTCCAAATGATCTTGTGGCAGTTCCTGTTGCAGGTTGTGCAGTAGCTGCCATAGATGGAGATGATCTTGGAGTAGACATTGTTGCTGGTTGAGAAGGTTGTGAAGATGGACCAGCCTAGTAAAATTCAAAAGAAGTTAGTAAAATTCAAGAGAAAATAGTAAAACTCATGTAAATCAATGAAATTTACCTTTGTTGTGTCCCTTTTTTTGCTAGTCTTCTTAAGATGGGCATTCTTCTTCTTGCCTCTCTCTGGATTTTGCTTGCAACCTTTCTTGTTATGTCCAGCAGTCCCACAGATTGAGCAAATAATTACAGTGCCATGCTTGGTCATTTTTTTGCTAGGCTTAGGTTTCTCTATTTCTTCCCTCCTCCTATCATTATTCTTAGGCCTGCCTGGCATGTTGTCTGGTATGGTTGCATATGCTGGGGCTTGAGGCCTAGGTTTGTCAGAAACTGGCCACATTTCTTCACCTTGTACAGGTTCCAAATAGTGTTCATAAATTTTGTTGAATACTTCAACAAAATAACAGGGAGCAATGAAATCTTCCACTTTTTTGCCACATTTGAAGATAGCTGTGCATGCATGGGAACAAGGAAGACCTGCCAGCTGGAAGTAGCCACATGAGCATGTCCAATTGTCAAGACTCACTGTGTACTGCCTTTTTCTCCCAGTGAGAAGTTTGACTTCAAATCCATCTTTTCCATTCCAAAGTACCTCCATGGACTGTGTCCTTGCTATGCTATTCTTCAACTTCTTAAAAGCACTGGGGCAGATTCTTCCATGAAACTTCTGATCTTTGGCCCTTTGTTCCTGAATTCTAACAAGTATTTGTTTCCTAATTTTTTCTTGCATTGAAATTATTGGATAAAACCTTGCTTCAACAATTGCATGATTAAAAGATTCACAAAGATTATTGTCAACTGATTCACAGTTGGAACCCACTAGAAAAAATGCCCTTGCCCAATGTACTGGCTCTGTTCTCATCATATCTTTTGCACCATCTGGTGTTTCTTGGGCTAGCTTTGCTTTGTAGTAGTTGAAGTCTTGCTTGTTTGCTGCTTTGGCAACTGCCCAGAACTTCTTCTGCCACTCATGTGCCCTATGCTTCTTTCTCCAGTTGGCATAGATATGCCTAGCACACATTCTGTGCTCTGCATTTGGCAGATAGTCCTGCATAGCATTAATCAGTCCCTTCTGCTGATCTGAAATGAACACCCATCCAGCTCCATTGTTATTAATGTCAAGATCTTTAATAAGCAAGCCAATAAACCACTTCCAGCTTTCATTTGTTTCCTTCTCAACAACAGCCCATGCCAGTGGATACATTTGATTGTTGGCATCTCTACCAACAGCACACAACAGCTCTCCTTTCACAGCTCCTTTGAAAAAACATCCATCTAATCCTATTACTTTCCTGCAGCCAGCCTTGAACCCTAACTTCAGTGCATTAAATCACACATAAAAGCTTTGAAATATGTTTTCTTCCATGTTTGTAGGATCCAAACAAACTGCAACAGTGCTTCCTGGATTACTTTTGAGCAGCTCCAATTGGTAATCAAAAACCCTAGTGTACTCATTCTTCATTCCAGCTCTTAATTTGTCCATGACTAGCTTCTTTGCATGCTTGCACTTAGAAGTTGATACATCAGCAAACATATCCTGGAGAACTGTTGCTTTGATGCTCTCAATCTTCCACATTGGATTAGCTAAAATGAAGTGCTCATATCTCTGAGCAATAACCTTTGCTGTCACAAGCCTGTTCTCTCTATTTTGTGCACATTCATGCTCATCATTAAAAGTAATAATCTGAAACCTGCTGGTTCTTGAGGTTTTGGCTCCATAAATCAACCAAGGGCACCCAGGCCATCCACACTTAGCTCTGACTCTATCTGCCTCTAATTTCATGAACACAATGCTCCTCTTGGTAACAATTCCATATCTCTTCAATGCCTTCACAAGCTGATTCTTGCTTCTGAACACCATTGTTAATGAGAAGTGTGGAATATCTGTGTCATTGTTGTATCTGGGATACTTGCTCTTCCTCCTAACCATTTGCCCATCAGAATCTTCATCATAAGAATAATCCTCATCAGATGAATCATAGCTCCACTCCTTCTCCTCTCCCTCTATCTGTTCTTCCATATTGGCAATTAGTTCAATGGGAACAGGTGCTGATGAATCTCCTGCAAGCCAACTCTTTGTATCTCTCATCTTCTTCTTGAATTTTCTAGCATGCCTCCTAAGCTCCACAACTTCAGAATTTTCTCCACTATCCTCACTATGGGGCATGTATTCAGTATCTTCATCAGAATCACTGTCTGAAACTGCAATATTGTCTTGCTCTGCTTCAATATTCACTTGCTCTCCTGCAATATTCACTTGCTCTCCTGCAATATTCACTTGCTCTCCTGCAATATTCACTTGTTCTGCTGTTGTACTGTTCTGAACATTGACTTGCTCTGCTCTTGTACTTAACTGAACTGGCACTTCATCTGGATTGCACACTTGAGAAATGACAAATTGGGAATCTGGCACTTGAACAACATCAGTAGCTTCTAAACTTCTTGTAGACCTGGGCTGCTTAACTGGACTGCTAACAAGTTGAGTGAGCACACCACTGTCAAGTGCCTCTGCACTAATGACAATATCAGGTTTTCAAATTCATCATCACTTACATCCATTATCTCATTCTCATAATCACTGCCACTACTGCTGTACTCACTGTCCTGCTCCCCATGATATTCAAGATAAATATCTGCTACATCTCCAACACAAATATAGTCTGCCATATTCATACAACCACTGTCATCAAACAAAAACACCAGACCCTCAGCTAGTTCCTTCCCAGGATACAGAAAATACAGCTTCATCGATTCCTTCAAATCAACATGGTCTTTCAAATGCCCTCTAACTTCTTGCAATGACAACTTGTCCCTCTCGATATGTGACATCTCTTCATCGCCCCCCACATAATCCAGAACAGGACCATTGTGGATGAACTGCCCTCCAATATGAAATCTGACGTTCAAAATCTCGTTCGGATCCATGATTTAACTGAAACAAACATGAGAATATCACTACATTGTCCTAATCCGAGCATTTGGAATAACAAAAATGCAAAAATAAAATCATCCCAAAACCTAACTTTACAGTTGACGAAAAGCCCCAATTTTTCGCCCACAAACCCTAACACTAACAGGGCAGAGAGAGCCTAAATTGCAGCGACCAGAGGAGGAGTACATCGAAGATATTACCTTCAACGCCGCTCGTCGTCCTG
+3355688 CTCAACTCTGACATTCCAAATAACCACATGGAAAAGGAAACGACCCCCCAAATTAAGAGACAGCTTCACTGAAGCAATGCTAGCTGTGACGTAATCTATAAGGTGTCGAGGGGGCTAGTGATTGATGCACACCTATTTAACTCATCTAGCATTTTGATAAGTTCACCGAAGAGATCATTGAGTAGGACACGCTTCTGCCTCTTGTATTTGTGCATTTTCCTCGGTGCTTTCTTCTTGCACTTGCTAACGGTGACATGCCTGCGAATTGAAAGCTACTACATCAGCAACAATGGAACACAGGCACAGCTCTCTTGCACAGTAGGTACGGTACACATTATGTTCATGCTAACAACATCTGCTATTGAGATGCTTGAATCACACTTCATGTTTCTATTTTCTAAATTAAAATAGACATCGGTACAGCAGAAAAGAAACACACAAATAGGTAGCCAAATTACCTCACAAAGCTATTAGCAAGGTAGTAGCAAAATCCTGAGCTCCATCCAGTTCTTGCTTCGTTTCCACTACGGCAAGCACTCCCTGCCGCTGAAATTGCTGATGAATATGATAGTGAAAAAACAGGGAATTGACCCAAGGAAGTATCCAGACTGTGTGCTATTCATTGGGAGGCGGCTGACTAACTAACTGTTGATGGAGTGGAAGAAGACCGCTGGCTTTCGAGCGGTGGTGCAGCCTGCTGTTGAGAAAGCCTGTTGATGGAGTGGAAGAGGACGGCGGTCCGGCCCTGCTACACCACCTCTTCTCTCTCTCCCTCTCATCTTCTCACCCCTCGCTCCTCCCCAGACGCCCCCACACTCTCCTCCTCCTCCTCCCCCGTCTCATCCACCCCTCCTCGTCCCGGATCCTGCCGGATCCGAGGCTTGTGGGCACGGAGGCGAGCTTCTCCGGCGCCGGCGTCGGTGCCGGTGGCAGCGGGAAAGGAGGCGGGGGTCGTGGGGGAGACACGCGGGCTAGGTCACGGGCATCGGCGGCGGCGGTAGGAGAGGAGGCAGGGGTCGCGGGGAAGACGCGCGGTAGCCAACGTGTTTTTTTGTCGGTACCTGTGATGACGTGGATAGCAGAAGGAGGCGCCCATGCCGCGACTATTAATGGGTTTAATTGCCAATTGCCCCACTCCCAAATTACTAGTGGATTCGATAGCACATTAGCATACATTAACGGAACATGTTTCCCTTATTGCCAATTGGCCACTTTAAGATTACCATCTGGGGAGGTCCGTTTAGTATCCCAAAACTGCTTAGCAAAAGTCGGACAAGTGGGTAATGTTGGGGTGAACCAAAAAAATTTGGGTAGAGCCGGATCTAAGTGTTGGCTAGGTAAACGCCCCGTAGTAAGAGGGGTAGTTATGAACCCTATGGACCACCCCCATGGGGGCGGTGAAGGGAAAGCTCCCATTGGTAGAAAAAAAAACCACAACCCCTTGGGGTTATCCTGCGCTTGGAAGAAGAACTAGGAAAAGGAAAAAATATAGCGATAGTTTTATTCTTCGTCGCCGTAAGTAAATACGTAACCAGGAATATGGAAAATTGCATTTTTGGAATTTGCAATAATGCGACGGGCGAACGACGGGAATTGAACCCGCGCATGGTGGATTCACAATCCACTGCCTTGATCCATTTGGCTACATCCGCCCCTTATCCAGCTAAAGGATTTTTTTTCTTTTTTCCATTGATAATTATTCTATTTATTCTGACCTCCGTACTTCGATCGAGATATTGGACATAGAATGCCACTCTTTAAAAAGGAAAAAAAAGGAGTAATCAGCTGTGACAGGAAAAAAACGAATCCTTTTGTAGCTCATCATTTATTGGCAAAGATAGAAAAGGTCAATATGAAGGAGGAGAAAGAAACAATAGTAACGTGGTCCCGGGCATCTAGCATTCTACCCACAATGGTTGGCCATACAATCGCGATTCATAATGGAAAGGAACATATACCTATTTACATAACAAATCCTATGGTAGGTCGCAAATTGGGGGAATTCGTGCCTACTCGGCATTTCACGAGTTATGAAAATGCAAGAAAGGATACTAAATCTCGTCGTTAACTGAATTCTGAATAGAAACATTAAGAAGAAGAAAAAGATTCAAAATAAAGACAGAAATACCCAATATCTTGTTCTAGCAAGATATTGGGTATTTCTGTCTTTTCTTTCTTCAAAAATTCTTATATGTTAGCACAAAAACCTTATCCATTAATAGATGGAACTTCAATAGCAGCTAAGTCTAGAGGGAAGTTGTGAGCGTTACGTTCGTGCATTACTTCCATACCAAGGTTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAAATTGGTTGAAATTGAAACCATTTAGGTTGAAAGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCCAAGCAGCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTTTCTTCATCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGGAACCATGCATAGCACTGAATAGGGAACCGCCGAATACACCAGCTACACCTAACATGTGGAATGGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGAGATTCCTAAAGGCATACCATCAGAAAAGCTTCCTTGACCAATAGGGTAAATCAAGAAAACAGCAGTAGCAGCTGCAATGGGAGCTGAATATGCTACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGCTACACAAGTAAGAAATGTAGAACAATTAGCTCATAAGGACCACCATTGTATAACCACTCATCAACAGATGCAGCTTCCCAAATTGGGTAAAAGTGCAATCCGATCGCCGCAGAAGTAGGGATAATAGCACCAGAGATAATATTGTTTCCATAAAGTAAAGAACCAGAAACAGGCTCACGAATACCATCAATATCTATTGGAGGGGCAGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCTGATGTAAAGACGATTTTCAGTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCACGTCTCTCTAAAATTGCAGTCATTGTAAGAACTTGGTTTATTCAAATTGCAAGGACTCCCAAGCACACGTATTAACTAGAATATAGATAATAGAAGGCTTGTTATTTAACAGTATAACATAGACTATATACCAATGTCAACCAAGTCAGCCCAAAGATTAGCTATCCATATAACTAAATTAACCAAACCAATAATTTTGTATTTGTAAATGAAGTGAGTCAAAGTTAAAAACTTTGATGGGTCTTTTCTATATGGGTTGCCCGGGACTCGAACCCGGAACTAGTCGGATGGAGTAGATAATTCTTCCTTGTTACAATAGAGAAAAATCCCTCCCCAAATCGTGCTTGCATTTTTCATTGCACACGACTTTCCCTATGTAGAAATAGCCAATTTCTATTCCAAAGAGGAAGTTCTACTAATTTTTTTAATAAGTAAGTTGATTCACCTACTCTTTATTATAATAAAAAGAACATTTCAGAATGAAAAATAGAAAAGTTTTTTCTTGATCATTTATTAACCCTTTCCTATTTCTTAATTTCGTCTAATGATTAATTAAGATGGTTGACCAGGTCATTGATACGTATAATATCCAAATACCAAATACGCTCAATGTGTGATCCACAAAAAGAAAAAAGAGTTGTTTTGGTGAACATCAAAGAAAAAACTTGCTCTTCTTCCATAAAAAATTCTTCTAAAAATGCCGAACCCAATCGTTGCATAAAAGTTCGTACCGTGCTTTTATGTTTACGAGCTAAAGTTCTAGCGCATGAAAGTCGAAGTATATACTTTAGTCGATACAAAGTCCGTTTTTTCGAAGATCCACTATGATAATGAAAAAGATTTCTACATATCCGACCAAATCGATCAAGAATATCCCAATCTGATAAATCTGTCCAAATGGGTTTACTAATAGGATGCCCCGATCCAGTACAAAATTGATCTTTTGATAAGTATCCTATGGGGAGAGTAGCGAGGACTATGGTATCGAATTTTTCATTCGAGTATCTATTAGAAATGAATTCTCCAGCATTTGATTCCTTACTAACAAAGAACTTTTTGGTACACTTGAAAGGTACCCCATAAAATCGAAGCAAGAGTTTGCTAATTGGTTTATATGGATTCTTCGCGGCTGAGTCTAAAAACAGAAATAATATTGCCAGAAATTGATAAGGTAGCATTTCCATTTCTTCTTCAAAAAAAAAGTGCCTTTTGATGCAAGAATTGCCTTTCCTTGATATCGAACATAATGCATACGAGGATCCATAAAGAACCATAGGGTTTTCCGAGAAAAACCAGGGTACATTATCCCAAAATGTTCCATCTTCCTAGAAAAGTGGATTCGTTCCAGAAAAGTTCCAGAAGATGCTAATGGTAAGCAAGAAGATTGTTTACGAAGGAACAACAAAAAAAATTCATATTCTGATACATAAGAGTTATATAGGAATCGAAATAGTCTTTTATTTTCTTTTTAGAAAAAAATGGATTTCATTGATGTAATAAAACTATTCCAATTCGAATAATAGTTGAGAAAGAATCGCAATAAATGCAAAGATGGAACATCTTGGATACGGTATTGAAGGAGTTGAACCAGGATTTCCAAATGGATAGGATAGGGTATTTCTATATGTGATAGATAATCCAAATGCAAAAATTTGTCTTCTAAAAAGGGAAATATTGAATGAATAGAGCGTAAATTCTGAAACTTTGGTATTTCTTTTTCTTTCGGACAAAATAATTCCCGTAGCGAGAATGGGATTTCCACAACGATCGCAAACCCTTCAGATAGAATCTGAGAATAAAACTCAGAATAAAAATTATTTTTGTAATCCAATAATCGATCTTGGTTAGAATGATTAACCGAGTTATCCAAAAAATTCTGCTGATACATTCGAATAATTAAACGTTTCACAAGTAGTGAACTAAATTTCTTGTTATTACAACTAACAACTATTTCCACAGGTTCAGAACCATTTAATCCATAATGGTGGGCAAATGCATAAATATATTCCTGAAAGAGAAGTGGGTAGACAAAGTATTGTTGACGAGATTTATGTTTTTCTGAATACCCTTCGAATTTTTCCATTTGTATTTCTACTTGAATCAGAGAGAAGAAGCATCTCTCGGTTTATCGAATGATGATACATAGTGCAATATGGTCAGAACAGGGTGTTGCATTTTTAATACAAACCCTGGAAAGAAAGGGAGTCTAATCCACAGATCTTTTTCTGCTCCTTTTCTACCCAATTAGTTTATGTTTGTTCTAATTAAAAAAAAGAACAGAACAAGTTTTTTATTTTTGCAGGCCAATCGCTCTTTTGACTTTGGAATACAGCCTCTTTATCAATATACTGCTTCTTTTACACATTCAATCCATAACATCCCTTATTCAATCCATAATCAAGAATAATTAGGATTTCTAAAAAAAGAAAAAATAAAGGGTCCACTCATAGCAAAACCCAACCTTTCCCCGCATCCGGCACTAATCTATTTTTAACGTCTAATTAGAGCGGGGAATCATTCCAATTAGGAAGTTCAGCTCGTTGCTTTTTATTTTACCAAAATTGGAGCCAGGCTCTATCCATTTATTCATTAGACCCAGAAAATCGTAATTTTGGATTCCATTCAAAAAAGATTGATTTAATTACGACATGCTATTTTTTCCATTCATTACCTTTGAGGATCAGTCGTGGTCTTCTAGACTCTACCAAGAGTCTGGACGAATTTGTTGTTTCATCCAAATGTGTAAAAGATCATAGTCGCACTTAAAAGCCGAGTACTCTACCATTGAGTTAGCAACCCAGATAAAAAAAGGATCTTAGATACGATCAAAATCCAAAAATCAATGGAATTACACCGCGCGCTTCTGTCAAAACATTGAACTAGCAAGACATCAAAAGATTTTTTTTATCGACCATGAAAAACACTCAAATGCCAAAACGAACAGGTCCGGTTAAATTCCACTAAAGTAAAGTTAAAAAAAGAGCGACCCTAATCATGATGGCCAAATTCTCCTTATTTTTAGCGATTTTTATTAAAAATATATATATATTATATTGTATGAGAATACATGCAAGAGGAACACCCTTATCATTTGAGCGAAGTGTAGGCGGAAAAATTGAATATGGAGTGAGGATAAAGAGACCCATCTATCTACAAATTCTATTTGTTCAATAGACCTTTGTTAATGGAAATACAATGGTAAGAAAACAAATTAGATAGAAAAAGTAAATAAAATAGGGGCTTATGTTGGATTGGCACGATATAATATAAATCCAAATAGGATTAAAAAAGAGGTAAATTGTGTCTAAATAATTAGACAACTAGGAATACTAATAATCTTCTCCTATCCTAATTTTTGATTCATTTAGTTCTTCAATTAACTCAAAGTTCTTTCTTTTTCTTTAAAGAATTCCGCCTTCCTTAAAATATCATAAACAGTTCTTGTTGGTTGAGCACCCTTTTCAAGGAAATAGAGAATAGCTGGAACATTTAAACAAGTTTGATTCTTTATCGGATCATAAAAACCTACTTTTTGAAGATCTCTTCCTCCTCTTCGAGATCGAACATCAATTGCAATGATTCGATAGACAGCTTATTGGGATAGATGTAGATAAACAACGCCCCCCCCCCTAGAAACGTATAGGAGGTTTTCTCCTCATACGGCTCGAGAAAATGATTAGAATTTCTGTCGATAATAATAGAAATTAGACTATGATGTGCATTAATTTCCTTACAGAAAAAACAAATTTCATTTATACTCATGACTCAAGTGGGCTAATTTTGCCTGACAAACTTCGAAGGCAAAATCCTTCCAAAAAATTTGAGTCGTCTTTAAACTCTTTTCTTTGTCTCATTTCGAACGAATTGACTTTTATTCCTTATTCTGATCCAACTCTGTTGTTGAGACAATTGAAAATTGTGTTTACTTGTTCTGGAATCCTTTATCTTTGATTTGTGAAATACTTGGGTTTAGACATTACTTCGGGAATTCCTATTTTTTTCTTTCAAAAGAGTAGCGACATACCCTTTTTTCTTATTTCCTTCGATAAAGCATTTATCTCTTCTATAGAAATCTAATAAGAGGGATTGATTCTGATATACTTTTATTGGACTTTCTTCTTATTTTAACCTTTCGATTTATTTCTATATTAAGGATAGGCTGACAAAGTTGGCCTAATTTATTAGTTTTCACTAACCCTAGATTCTTTCCCTTGATAAAAAAATTCTGTCCTCTCGAGCTCCATCGTGTACTATGTTACTTAAACCCAGCGCAAATTTGGTTCGGAACGAATAGAACAGGCTATGTCGAGCCAAGAGCATTTTCATTACTATGGAAAATGATGGATAGAAAAATCCACAATCGATCATGTCCTTCAAGTCGCCCGTTGCTTTCTACCACATCGTTTTAAACGAAGTTTTACCATAACAAACATTCCTCTTTTCATTGCAAAGTGGTATAGAGAATTGATCCAATATGGATGGAATCATGAATAGTCATTGGTTTAGTTTTTTTATACTAATTAAAACTTGCTATCTATGGAGCAATATGGATAAAAGAAAGTAAGTATTTATCCGGGAAGCCTCCACCAAGATCCAATTTATTTAAACCCATATTAAAATTCTATCATATGAATGAAACATCGTTTGAAAAAGACGACTAAACAAGTTTGCTTAAAACTTATTTATTCTTAAATTTCCACCCTCAACGGATGGCTCGAGATGATCAATCTTGAAGTGAGAAAAGAAGGATTGACTCTTCCTCAATAAATAAACTATCAACCTCCAAAAAAGTTTAATTAATTTAATTACTAGAATTAGAATTCTAGTAGTAATATATTTTTTAGTACCAAAAACAATTAAAAGTAAATAAACTATTCCAATGAAAAGATTGAAAGTTTTTGGTAGTTATAGAATTCTTGTACTTCTTCAACTCGAATACCAAAAGGAAGAAAAAAATATGACTAAGTGATTTTATAGTAGAGGCATATCCTGAATGTGCTTGATAGATCCCATTTTTTCATGAAAATAAAGATAGTCAATTTGACTGGACTTAAGACTTTATTATGTTTTCTGAGAAAGAATAAGATATCATTATTCTCTTTAATAAACTTTTGTCTCGTACGGAATACTATATGATTTCACCATTTGTTTCATCAGAAACAATCTGGGACGGAAGGATTCGAACCTCCGAGTAACGGGACCAAAACCCGCTGCCTTACCACTTGATCACGCCCCATTTCGGGTTTTATGCGACACTAATAAACACTAATATGTTTATTTGTTATTCGTCAATACCATTTCAATTACATAAAAAAGGAGGGATATTCTCTTGCTAGTATTCTACACATGCGGATAATATAGAATCAAAAAAATGCATTGATCATTACATGGAATTCTATTAAGATATTATATGAAAGTCGAATTTATTCCACTCTCATTTGAGAGTGCGAATACAAGGAGGTATTTTGTGTTTGGGAAAGTCCGAAGAAAAAAGATTTTGAATCTGCCTTTTCCTTCTTTCCCTTAAAAAAATAACTCAAGAAAAATCCAATTATTTACTCTACAAGAATGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTCTGTTCTTTATCCTACTAGTTTTTTTCTTTGCCAAATTACCCGAAGCTTATGCTATTTTCAATCCAATCGTGGATATTATGCATGTTATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTCTAAGTTTTCGATGAAATCTTTAGTACTCTGTATGCCAAATTGAATGATGTGTTCATTCCAAAAAAAATTAAAAATGGGTAAAAGCCGAGAAGTTTTATATTTTTATATTATGAACCTTTGATTCTAAAATTTAAATTCTTCTACATTGAATGGGTAGCTACAGCAATAAATTTGGATCAGCCTTTCTACTCCCCTGCACCTAGGTTGAGCAGGTACCTAAAGGTACCTACACAATACCTAACCACCTAACCCTATTTTTGCTATTGATAAGAGTGCTTATTATAAAAGAATTCTTGCAATTTTTTCAAGAATTCTTTTTTGCATTTTTAGGTATAAAAAAAACCATCCTAGTGGATCCGTGTGGTAAGGAAAAACTGGTAATCTATTCCTTAAAAAAAATCTTGGAGATTATGTAATGCTTACTCTCAAACTTTTTGTTTATACAGTAGTGATATTCTTTGTTTCACTCTTTATCTTTGGATTCTTATCTAATGACCCAGGACGGAATCCTGGACGCGAGGAGTAAAAATTCAGTTTTTTTTCTTATTGGATTTGTTTCGTACATTTATCTATGAGAAAATCCGGGGGTCAGAATTCTTTCCAATTCGAAAGTCCCAAATGATCCAAGGGAGCGGAAAGAGAGGGATTCGAACCCTCGGTACAAAAAAATTGTACAACGGATTAGCAATCCGCCGCTTTAGTCCACTCAGCCATCTCTCCACGTTCCAAAGCGAAAGGTTTCCGTGATATGATATAGGCAAGAAATAAGAAATAACGGTTGCAAAAAACCCCCTTTTTTCAAAAGTCTATAAAAATTATATTGCCAATTCCATTTTAATTATATTATTTTTTCTTAATGTTAATAAAAAAAGAAGAAAATTCTTGTTTTTTCTTTCTAAAAATCGATATTGGCCGAGAGACAATCAAATAGATTTTCTCTTTAGCGGGCATTTCAATATAGGACTTGTTATAATTATAATAAAACAAGCAGGTTATATAAAAAAACGCTTTTTGTCGATTATTTATCAAGAAAGCAAAAAGGGTTCTTATCAAATCCACCATAAAATTGGAAAGAAGCATAAAGTAAGTAGACCTGACTCCTTTAATGATGCCTCTATCCGCTATTCTGATATATAAATTCGATGTAGATGAAATTGTATAAGCGAATTTTTTTTATTTCCTTAGACTTAGACCGCGCAAGACAAGAATTTTGCGCTATTTACGATTTCATATTCTTGTTACTAGATGTTCTATAGGAATAAGAAGAAATCGCAACTCCTTTGCGCTACACATAAAATTGGATTTCGAAGGTCCATTTTTTTATAGGAATCCTCTATTTAGTTCTTCCACCCATGCAATAGAGAGGGAATGGGAAAAGAAGGGTTACTTTTATTTTCATTTTTCCCTTAAAAGATAGACTTTGAAATAGGAGTCTTGGAATAATGCTGAATTCAAAGGTTTATTTCTTTCTATAGTATAAAAAAACAATTTATTTCTATTTCTATAGTATAAGAAAAACAAATAGTATAAGAAAAACAAATCGAATCAAATTCATGGATTTACCACGACCTCGGTTGTGACTGTGACTCCATAGATAAAAATGGGAAATTTCTCTCTTCGAGACCATTGAAAAAGGGCATTGAACGACAAAGAAATCGTCCACAGATAATAAAACTATCATATGCCTTGGAAAGTGATATGAGGTGCTCGAAAATGGTTGAAGTAATTGAATAGGAGGATCACTATGACTATAGCCCTTGGTAGAATTCCTAAAGAAGAAAATGATCTATTTGATACTATGGATGACTGGTTACGAAGGGACCGTTTCGTTTTTGTAGGATGGTCTGGCCTATTGCTCTTTCCTTGTGCTTATTTCGCTTTAGGGGGTTGGTTTACAGGGACAACTTTTGTAACTTCTTGGTATACCCATGGATTGGCTAGTTCCTATTTGGAAGCTTGTAATTTCTTAACCGCAGCAGTTTCTACCCCTGCCAATAGTTTAGCACACTCTTTGTTGCTACTATGGGGGCCCGAAGCACAAGGAGATTTTACTCGTTGGTGTCAATTAGGCGGTCTATGGACTTTTGTAGCTCTCCACGGGGCTTTTGCACTAATAGGTTTCATGTTACGCCAATTTGAACTTGCTCGGCCTGTTCAATTGCGGCCTTATAATGCAATCTCATTCTCTGGTCCAATTGTTGTTTTTGTTTCTGTATTCCTTATTTATCCACTGGGGCAATCTGGTTGGTTCTTTGCGCCGAGTTTTGGCGTAGCAGCGATATTTCGATTCATCCTTTTCTTCCAAGGATTTCATAATTGGACGTTGAACCCATTTCATATGATGGGAGTTGCCGGAGTATTAGGTGCGGCTCTGCTATGCGCTATTCATGGAGCGACCGTAGAAAACACTCTATTTGAGGACGGTGATGGTGCAAATACCTTCCGTGCTTTTAACCCAACTCAAGCTGAAGAAACTTATTCCATGGTCACTGCTAACCGCTTTTGGTCCCAAATCTTTGGTGTCGCTTTTTCCAATAAACGTTGGTTACATTTCTTTATGCTATTTGTACCCGTCACCGGTTTATGGATGAGTGCTATTGGCGTAGTTGGCTTGGCTCTGAACTTATGTGCCTATGACTTTGTTTCCCAGGAAATCCGTGCAGCGTTAGATCCTGAATTTGAGACTTTCTACACCAAAAATATTCTTTTAAACGAGGGTATTCGTGCGTGGATGGCAGCTCAGGATCAGCCTCATGAAAATCTTATATTCCCTGAGGAGGTTCTACCACGTGGAAACGCTCTTTAATGGAACTTTCATTTTAGCTGGTCGTGACCAAGAAACCACCGGCTTTGCTTGGTGGGCTGGGAATGCCAGACTTATCAATTTGTCTGGTAAACTGCTTGGAGCTCATGTAGCCCATGCCGGATTAATCGTATTCTGGGCCGGAGCAATGAACCTATTTGAAGTGGCCCATTTCGTACCAGAAAAGCCCATGTATGAACAAGGGTTGATTTTACTTCCACACTTAGCTACTCTAGGTTGGGGAGTAGGGCCGGGGAGGGAAGTTCTAGATACTTTTCCGTACTTTGTATCTGGCGTACTTCACCTAATTTCCTCCGCAGTCTTAGGCTTCGGTGGCATTTATCACGCGCTTCTGGGACCCGAGACTCTTGAGGAATCTTTTCCATTCTTTGGTTATGTCTGGAAAGATAGAAATAAAATGACTACAATTTTGGGTATTCACTTAATTTTGTTAGGTCTAGGTGCTTTTCTTCTAGTACTCAAGGCTCTTTATTTTGGCGGTGTATATGATACCTGGGCCCCTGGGGGGGAGATGTAAGAAAAATTACCAATTTGACCCTTAGTCCCAGTGTTATATTTGGTTATTTACTAAAATCTCCTTTTGGTGGAGAAGGGTGGATTGTTAGTGTAGATGATTTAGAAGATATAATTGGTGGGCATGTATGCATGGTTGGGTTTTATTTGCGTATTTGGCGGAATTTGGCATATTTTAACCAAACCCTTCGCATGGGCTCGCCGTGCATTTGTACGGTTTGGAGAAGCTTACTTGTCTTATAGTTTAGCTGCTTTATCTGTCTTTGGTTTTATCGCTTGTTGTTTTGTATGGTTCAATAATACAGCTTATCCGAGTGAGTTTTATGGACCCACCGGGCCACAAGCTTCTCAAGCTCAAGCATTTACTTTTCTAGTTAGAGACCAGCGTCTTGGAGCTAATGTGGGATCCGCTCAAGGACCCACAGGTTTAGGTAAATATCTAATGCGTTCCCCAACTGGGGAGGTTATCTTTGGAGGGGAAACTATGCGTTTTTGGGACCTTCGTGCTCCATGGTTAGAACCTCTAAGGGGCCCCAACGGTTTGGACTTGAGTAGGTTGAAAAAAGACATACAACCTTGGCAAGAACGACGCTCAGCAGAATATATGACCCACGCTCCTTTAGGCTCTTTAAATTCCGTGGGTGGCGTAGCTACCGAGATCAATGCAGTTAATTATGTCTCTCCTAGAAGTTGGTTATCAACTTCTCATTTTGTTCTAGGATTCTTCTTTTTTGTGGGCCATTTATGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGATTTGGAACCTGTTCTTTACATTAACAGTCGCGGCATGGGCGCCTCCTTCTGCTATCCACGTCATCCAGACTGTTAAAAGACTGTTAACGGAACGGCTAACCGGATATTATCGACCGTGCTCCAGAAAATAAGGGAAAGTGGAATTCTTTTGTGTGTCTGTTTGGTGCTGGACTTCGGCTAGCTAGGTAGGAGAGTCAAGATAAGTATTGACAGTGTTGAGCTCAATGTACTTATGAAATCACAATCTGTACTTATGAGATCACAATGTGTACTTATGAAATCACAATCTGGATCGCGCAGTAAATTAGTGTATATACTCCTGGCTCTCTTCTTTCAAGATGGATTCTGTTATGATACTACCCCCTCAATCCCAACCCCAGTGCTTTCACCAACTTTGCCAAACAGTGACATTATCATGGGCCAAAAACATATGCTAATCGTAACTATTATATCTTGATAGAGACACGCATAGAAGGAAATGAGACTGTATATAGATTAAGCGGAGACTGTCAGCGTCGATTCAGGTGACGCGGAGGTGAGAAAAGACGCATGATTTGGCGTCGCGATCCGCCGGCACGCATCATGTGCCGCGCAGCCAGATATATCCACCAGAGAAGGGTCACAAGCCATCCTGCCATGCCATGATGCCATGGCCACCGCCATGAGTGGATGAAATGAATGGCTGAATCAGAGGGCCGGGAAGCAGCTAGCCCAAGAAAGGACCGAGGTGTGTAAGCCTTCTCGTCTCCCAATGGACGAATTGAAGTGGAGTGGAGGAGCTGCATGCATGCCAATTGCTGCTGTCCTAGAATTACTGTTCATTCATTTCGTGGCTCCCTAGAGATTCTTCGCGGAAGAGACAAGAGCATACTGCAGCGAGCATATGGGCATACGGGGGTTCGTCGTTGGATGGAGCGCAGTGCAGGGAAGATCAGATCAAAGGAGGAAAAGAATTGAAGGCGCGCATTTGCACGGGAGACGCACGCTGCAGCAACATTTATGCTGCCTGCAATCGAGGTTGATGCAGCCTTCTTCTTGGATGGACGGCCGTCCGGCAATGGGGTCGTAGTAACTGTTGTTGTCTCATTACTGTCCACCTGTGCCTGTGTGCACTGCAACTGCATACATATTGTGGCATACAAATGCATTGAACAAAAGTCAATCGAGAAATTCGAGATCGAGCGGCGGCAGGCAGATGGCCAAGCATTTTTGCGTCCAAAAGCTAAGAAGATTTCAGTGGGAATTTCGCGCTCGCTCGCACTCGACGGCAAAGCATATTCGTCTTCGATACGTACTGCTCATCATGCATGGTACTTCTGCTTTCCGAAAGCAGCTGCTAGCTGGGCCTCTCCTGTCCCGTCCCGGCGCTTTGAGCAACATCGAAACAGAGAGCTACTACCACGAGATATGCTTGTTTGTTTATAGGATGGGATGGAAGGGGAAACAAAAATGCTGAATTCCACATGATGAATTCCTGTCGGCTTCGTTTCTAGGCAGCTACCATTGCAGTACTAGCATATAGCACCTACGTATGGAATTCCATAGAAGAGGAACACACTCTCTTCCTTTCAAGTGCTCCCTCCGTCTCAAAAAACTTGTCCCTCAAATGGATATATCTAACATCAAATTAGTGCTACATACATCCATTTGAGGGACAAGCTTGGGATAAGCTTTTTCGGACGGAGGGAGTACTAATTTGTAGGTTGTTTTTAACTTTAAAAGGCACGGACTACTTAAAAGAGCGAAATACAATTTGTTTCAAATTTGAAGGTGGCGCCAAATATGCAGTGGTGTTGGTGGTGGAGCACATGCATGTCTTCACGCAGTGCAGTGAAACAGAGCATCGCAGGCAGTATATATGCAGTGGTCCTTTTCTCCCTCTCTCAAAGTTACTTTTCCTAATCCAGAGATGCAGTTGCAGGCCACTTTCCTCCCGCAAAGCCGTCGATCAGTGTAGGCGTGTAGCTCAGTACCATCGCATTACTGCATACTAGTGGGAAAAAACGCAACAGGACCCTTTGAACTTGACAATGCAATTTCGTCTTCAGTTTTCTCGGATCTGACCCATTTTTCTACAAAAACTGCACCATTTCTTTGCCATGATAGAGAAGAAGCTACTGCTCGCAAAGAAATTTTGTGGGAACCATTGGCTCGTCTCAAAGCAAGTGAGGATAGACCATGTGGACGGATCGAGGATGATTGTACAAACCTTTTTGTTGCTTTCTTCACTGAGACGGCGATCTGGTTTCATTGTCACCGGCTACTTCTGGCTTCAACTTGTGACTTCCTGACCACTGCATCAACATTGTTACCCCGGCTCCGAGGACGTTTTGGAGATATAAAGGCAGCATCGAGCTTTGCCCATAGTGCGCTACCGGCGAATGCAGGAGTATGGAATATCTTTTTTATACTTGGATTGTATACTTGAGTACTGAAACTTTGTGTTCCTCGTATTGCAAACAGCATGGAATTACATAACTAATACGCGTGTCGATCGGGTTCCGAACAACCTCTGTTCACATTGGTGGTACGGACGAGACCACAGGGAGGTTTCATATCTCTCGATCAAAAGAGCAATGCTGCTTTTTCCCTGGGTATAGAATAGGAATCAATTCGTTTTGCAACGAATCTCGAGACGAGGAAAGGTGGCTTCTTTGGCATTTTGCTGAGCTGGTATGTACCGTGCCGTCCAAGGTTTGGAATATGGTCGGCAATGGATAAGGTAGATCACATGGTTTGGCACCCAACTATTCTTCTCCTCTCACCTGAGGCGGCAGAGCTAGCTAGCTACAGTTTATAGCACGAATGATCACACTATCGTTTTCTTTGACAAAAAAATAAAATAGTTTCGTTATCCATATCTATCCGAGTCAAAATAGCATTAGCTAGCCCTTGGTGTAATCATGGCGATGATGAACCGATCCAAGGTGATTTAGTAGTATTTTAATCTCGGCGAGAGGATTCAGAATCAGAAAGATATTCTTGTCCTCGCAAGGAGAAAAAAGAGGACGAGGGGTGAGCAGTTGGGATTTGGGAGCAGGGCGAGGGAGGCCTGATTGCTCAATGAATGGCATATCCTCCTGTCCTTTTGCCCCCTGCTGACCGATGGATGGATACGACGCCACTGCGAGAATCCTCATGATCCCACAGATGCCTCACTCTCTCTGATCCTATCCAGGCCACCTCATCATGGAACTGATGAGGATTTCGTGTATTAGTTGAGCAAAATTAGGTTTCTCTTTCTAACTCTAGCTAGTATATATGTGACACAGGCAGCTGCTGCTAGCCACCCCATGTATGGAACTTTTGTTCCCATTAACAAAACATCCCCTTCGTATTATTTTTTATGTGTCTAGTTGTGCGGAAAGATCAGCTAATCTAGGGCCTTAGGGTTCTTAACAATTAAATTAGTTTTGTGCTTAATAATTATTTAATTTGGAAATGGACGTACGTTTACGTAGGAGTATCATACATGGTGGTGATTACCATGATGACACCCACAATCAGGTGATCCGTCTTGCCCTCCGTTTCCTTTTCGCTTTAGCTACTCCTCAATCACCTGAAAACTACTCCGTTCCTAAATACTCCCTCCGTTCCTAAATACTTGTCTTTCTAGGCATTTCAAATGACTATCACATACGGATGTATGTAGACATATTTTAGAGTATAGATTCACTCATTTTACTCCGTATGTAGTCACTTGTTGAAATGCCTAGAAAGACAAGTATTTAGAAACGGAGGGAGTACTTGTCTTTCTAGGCATTTCAAATGACTATCACATACGGATGTATGTAGACATATTTTAGAGTGTAGATTCACTCATTTTACTCCGTATGTAGTCACTTGTTGAAATGCCTAGAAAGACAAGTATTTAGGAACGGAGGGAGTACTTGTCTTTCTAGGCATTTCAAATGACTATCACATACGGATGTATGTAGACATATTTTAGAGTGTAGATTCACTCATTTTACTTAATATGTAGTCACTTATTGAAATGCCTAGAAAGACAAGTATTTAGGAACGGAGGGAGTATTCAGGATTAGTCGATTTTTTACCCCCACCGCTTCATGCACGTGATGAGCACTACAGCGTGCTTGCAGCATGCAGCTGATGCATGCAAGCTCGCTTAATCAGCATGACTATTAATCACTAGACGTCTGACAGGCGGCCGAGAATTTTAATGGCATCCGTGTTAGTTTAAATTCAAAATTAAATAAACTTGTTTGTCATCTCTTCCTTCTGGTATCCTGACTAACTTGCGCAAGGTACGTCGACCTAGCTATATAGCAAAGCCAAAGTGACATGTAATCTCAGAAGGTTAGCCATCACTCTCCACAAATAAAGGACAAAGCAAAATCTGAAAAACAAAATAAAGGAACAATATCAAGAAAAGAAGAAGAGAAAAAAAAGGCAAAAGGCTTGTGTCAGCTGCGCTCTACTCACTCGACAATCATGCATGGTACCAATACGAATTATGGTGAGGTGTAGTTAGTGAACAGAAAACACGAAGTCTGCATGTGACTGGCCAAACACGCACGCACCTGCATACGTGACAACACTAAAGCAGGATCTCTCATGCAACACAGCAACGTACTGGAATATTTCGATGGAGTGGTAAGGCCAACTCCACCGCGTGACCCCAAATGGACTTCTGTTTTGTTTGGATTCTGTCCGTTTGGATAGGGATTTGGGGTCGTGTCCAGGTGTGTCCTGGGATGCGGTGGCCGTGCGCCCGCGCGCGGCTGCATCCATTTGCCCCATCCTGTCCGTCAGGGCCAAAAATGCCCATATTCTCATCAAAACTAGTTTGCACGTCCAAATATTTGTCTGAAAATTAAAATAGTTTTACAACCCAATTGAAATTGTCCTTAATAAAAAAGTTTTACAACCAAATCGAAATTGTCTTGACTGAACATAAAATGAACCAATACGTCTACTGGTTGCCAATGTGATCCCACACATGCTCAACCAAGTCATTTTGAAGATTCAAATGACTGTGCCAATCACGCATCTCACGGTGGAATTGCACAAATTGTTCAAATGTGGCCGGGTCTTGGTGCAGGGGCTCAATATTTTCACCTTGATAATCAAATCCTTGGTCGAAGATACTCTCATCACGCTCGTCCTCGACGATCATGTTGTGCATGATCACACAAGCA
diff --git a/modules/t/test-genome-DBs/polyploidy/core/dna_align_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/dna_align_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/exon.txt b/modules/t/test-genome-DBs/polyploidy/core/exon.txt
new file mode 100644
index 0000000000..15c044ce95
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/exon.txt
@@ -0,0 +1,13 @@
+243045 3495727 1206 1416 -1 0 1 1 1 Traes_6DS_3B68FB2E11.E1 1 2014-01-21 14:05:47 2014-01-21 14:05:47
+243046 3495727 898 1040 -1 1 0 1 1 Traes_6DS_3B68FB2E11.E2 1 2014-01-21 14:05:47 2014-01-21 14:05:47
+243998 3495727 8829 9015 1 -1 -1 1 1 Traes_6DS_F1A510F0D1.E1 1 2014-01-21 14:05:48 2014-01-21 14:05:48
+247713 3495727 1853 2068 1 0 -1 1 1 Traes_6DS_262C704652.E1 1 2014-01-21 14:05:56 2014-01-21 14:05:56
+357233 3495794 3573 3641 -1 1 1 1 1 Traes_5AL_7256A9F19.E16 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357234 3495794 3415 3475 -1 1 2 1 1 Traes_5AL_7256A9F19.E22 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357235 3495794 2985 3124 -1 2 1 1 1 Traes_5AL_7256A9F19.E14 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357236 3495794 1327 1486 -1 1 2 1 1 Traes_5AL_7256A9F19.E17 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357240 3495794 3854 3957 -1 2 1 1 1 Traes_5AL_7256A9F19.E18 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357242 3495794 4455 4791 -1 -1 2 1 1 Traes_5AL_7256A9F19.E20 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+357243 3495794 506 1129 -1 2 -1 1 1 Traes_5AL_7256A9F19.E10 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+379407 3495644 2408 2611 -1 0 0 1 1 Traes_6BS_5FDE5650B.E1 1 2014-01-21 14:18:24 2014-01-21 14:18:24
+382466 3495644 2030 2272 -1 0 0 1 1 Traes_6BS_48A5D59CE.E1 1 2014-01-21 14:18:30 2014-01-21 14:18:30
diff --git a/modules/t/test-genome-DBs/polyploidy/core/exon_transcript.txt b/modules/t/test-genome-DBs/polyploidy/core/exon_transcript.txt
new file mode 100644
index 0000000000..a450a613bc
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/exon_transcript.txt
@@ -0,0 +1,13 @@
+243045 79141 1
+243046 79141 2
+243998 79459 1
+247713 80726 1
+357233 116850 3
+357234 116850 4
+357235 116850 5
+357236 116850 6
+357240 116850 2
+357242 116850 1
+357243 116850 7
+379407 123920 1
+382466 124987 1
diff --git a/modules/t/test-genome-DBs/polyploidy/core/external_db.txt b/modules/t/test-genome-DBs/polyploidy/core/external_db.txt
new file mode 100644
index 0000000000..2608af6a3d
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/external_db.txt
@@ -0,0 +1,612 @@
+210 Anopheles_symbol \N KNOWN 50 Anopheles symbol MISC \N \N \N
+211 VB_Community_Symbol \N KNOWN 50 VB Community Symbol MISC \N \N \N
+212 VB_External_Description 1 PRED 50 VB External Description MISC \N \N \N
+213 VB_RNA_Description 1 PRED 50 VB RNA Description MISC \N \N \N
+230 Ribosomal_Protein_Gene_Database Dec.2010 XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
+250 ImmunoDB 1 KNOWN 50 ImmunoDB MISC \N \N \N
+300 BRIGGSAE_HYBRID \N KNOWNXREF 5 Briggsae Hybrid MISC \N \N \N
+400 Celera_Gene \N PRED 5 Celera gene MISC \N \N \N
+410 Celera_Pep \N PRED 5 Celera peptide MISC \N \N \N
+420 Celera_Trans \N PRED 5 Celera transcript MISC \N \N \N
+600 DROS_ORTH \N ORTH 5 DROS ORTH MISC \N \N \N
+700 EMBL \N KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
+701 EMBL_predicted \N PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
+800 flybase_gene_id \N KNOWNXREF 5 Flybase Gene MISC \N \N \N
+801 flybase_translation_id \N KNOWNXREF 5 Flybase translation ID MISC \N \N \N
+802 flybase_gff \N KNOWNXREF 5 Flybase GFF MISC \N \N \N
+803 flybase_polypeptide_id \N KNOWNXREF 5 Flybase Polypeptide ID MISC \N \N \N
+804 flybase_annotation_id \N KNOWNXREF 5 Flybase Annotation ID MISC \N \N \N
+805 flybase_symbol \N KNOWNXREF 50 Flybase Symbol MISC \N \N \N
+806 flybase_synonym \N KNOWNXREF 5 Flybase Synonym MISC \N \N \N
+807 flybase_name \N KNOWNXREF 5 Flybase Name MISC \N \N \N
+808 flybase_transcript_id \N KNOWNXREF 299 Flybase transcript ID MISC \N \N \N
+810 gadfly_gene_cgid \N XREF 10 Gadfly gene CGID MISC \N \N \N
+811 gadfly_transcript_cgid \N XREF 10 Gadfly transcript CGID MISC \N \N \N
+812 gadfly_translation_cgid \N XREF 10 Gadfly translation CGID MISC \N \N \N
+821 FlyBaseName_gene \N KNOWN 5 FlyBase gene name MISC \N \N \N
+824 FlyBaseName_translation \N KNOWN 5 FlyBase translation name MISC \N \N \N
+825 FlyBaseName_transcript \N XREF 50 FlyBase transcript name MISC \N \N \N
+826 FlyBaseCGID_gene \N XREF 5 FlyBase gene CGID MISC \N \N \N
+827 FlyBaseCGID_transcript \N XREF 50 FlyBase transcript CGID MISC \N \N \N
+828 FlyBaseCGID_translation \N XREF 50 FlyBase translation CGID MISC \N \N \N
+829 BioGRID \N KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
+830 FlyExpress \N KNOWNXREF 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis MISC \N \N \N
+831 GenomeRNAi \N KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
+832 InteractiveFly \N KNOWNXREF 5 The Interactive Fly MISC \N \N \N
+833 MitoDrome \N KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
+880 BDGP_insitu_expr \N KNOWNXREF 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC \N \N \N
+882 FlyGrid \N KNOWNXREF 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC \N \N \N
+883 FlyReactome \N KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
+890 DEDb \N KNOWNXREF 5 Drosophila melanogaster Exon Database MISC \N \N \N
+900 GKB \N XREF 5 GKB MISC \N \N \N
+1000 GO GOA UniProt (version 136), released on 29 October, 2014 and assembled using the publicly released data available in the source databases on 25 October, 2014. XREF 5 GO MISC \N \N \N
+1001 GO_REF \N KNOWN 5 GO Reference Collection LIT \N \N \N
+1100 HGNC \N KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+1200 Interpro \N XREF 5 InterPro MISC \N \N \N
+1300 EntrezGene \N KNOWNXREF 250 EntrezGene MISC \N \N \N
+1400 MGI \N KNOWNXREF 270 MGI Symbol MISC \N \N \N
+1500 MIM \N KNOWNXREF 5 MIM MISC \N \N \N
+1510 MIM_GENE \N KNOWNXREF 5 MIM gene MISC \N \N \N
+1520 MIM_MORBID \N KNOWNXREF 150 MIM disease MISC \N \N \N
+1600 PDB \N KNOWNXREF 5 PDB MISC \N \N \N
+1700 protein_id \N KNOWNXREF 5 INSDC protein ID MISC \N \N \N
+1701 protein_id_predicted \N PRED 4 Predicted INSDC Protein ID MISC \N \N \N
+1800 RefSeq_dna \N KNOWN 200 RefSeq DNA MISC \N \N \N
+1801 RefSeq_mRNA \N KNOWN 200 RefSeq mRNA MISC \N \N \N
+1803 RefSeq_ncRNA \N KNOWN 200 RefSeq ncRNA MISC \N \N \N
+1805 RefSeq_dna_predicted \N PRED 199 RefSeq DNA predicted MISC \N \N \N
+1806 RefSeq_mRNA_predicted \N PRED 199 RefSeq mRNA predicted MISC \N \N \N
+1808 RefSeq_ncRNA_predicted \N PRED 199 RefSeq ncRNA predicted MISC \N \N \N
+1810 RefSeq_peptide NCBI Reference Sequence (RefSeq) Database Release 68, November 3, 2014 KNOWN 210 RefSeq peptide MISC \N \N \N
+1815 RefSeq_peptide_predicted \N PRED 197 RefSeq peptide predicted MISC \N \N \N
+1820 RefSeq_rna \N KNOWN 230 RefSeq RNA MISC \N \N \N
+1825 RefSeq_rna_predicted \N PRED 195 RefSeq RNA predicted MISC \N \N \N
+1830 RefSeq_genomic \N KNOWN 193 RefSeq Genomic MISC \N \N This external_db_id can be used in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The RefSeq_genomic is stored as a synonym. eg. NC_000011.10, NT_187365.1
+1900 Sanger_Hver1_2_1 \N XREF 5 Sanger Hver 121 MISC \N \N \N
+1901 Sanger_Hver1_3_1 \N XREF 5 Sanger Hver 131 MISC \N \N \N
+1902 SNGR_Hver \N XREF 5 Sanger Hver MISC \N \N \N
+1910 Sanger_Mver1_1_1 \N XREF 5 Sanger Hver 111 MISC \N \N \N
+2000 Uniprot/SPTREMBL \N KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
+2001 Uniprot/SPTREMBL_predicted \N PRED 117 Predicted UniProtKB/TrEMBL MISC \N \N \N
+2010 prediction_SPTREMBL \N XREF 10 Prediction UniProtKB/TrEMBL MISC \N \N \N
+2100 Superfamily \N KNOWNXREF 5 Superfamily MISC \N \N \N
+2200 Uniprot/SWISSPROT \N KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
+2201 Uniprot/SWISSPROT_predicted \N PRED 15 Predicted UniProtKB/Swiss-Prot MISC \N \N \N
+2202 Uniprot/Varsplic \N KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
+2250 UniProtKB_all \N XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
+2300 Vega_gene \N KNOWNXREF 5 Vega gene MISC \N \N \N
+2305 Vega_gene_like \N XREF 5 Vega gene like MISC \N \N \N
+2310 Vega_transcript \N KNOWNXREF 160 Vega transcript MISC \N \N \N
+2315 Vega_transcript_like \N XREF 5 Vega transcript like MISC \N \N \N
+2320 Vega_translation \N KNOWNXREF 5 Vega translation MISC \N \N \N
+2400 wormbase_gene \N KNOWN 5 WormBase Gene MISC \N \N \N
+2410 wormbase_transcript \N KNOWN 5 WormBase Transcript MISC \N \N \N
+2420 wormpep_id \N KNOWN 5 Wormpep ID MISC \N \N \N
+2430 wormbase_pseudogene \N PSEUDO 5 WormBase Pseudogene MISC \N \N \N
+2440 wormbase_locus \N KNOWN 5 WormBase Locus MISC \N \N \N
+2510 ZFIN_ID \N KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
+2530 ZFIN_xpat \N KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
+2600 GeneDB \N KNOWN 5 GeneDB MISC \N \N \N
+2601 cint_jgi_v1 \N KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
+2602 cint_jgi_v2 \N KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
+2610 cint_aniseed_v1 \N KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
+2611 cint_aniseed_v2 \N KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
+2700 Ens_Hs_gene \N XREF 5 Ensembl Human Gene MISC \N \N \N
+2710 Ens_Hs_transcript \N XREF 170 Ensembl Human Transcript MISC \N \N \N
+2720 Ens_Hs_translation \N XREF 5 Ensembl Human Translation MISC \N \N \N
+2800 RGD \N KNOWNXREF 50 RGD Symbol MISC \N \N \N
+2900 Genoscope_pred_gene \N XREF 38 Genoscope pred gene MISC \N \N \N
+2910 Genoscope_pred_transcript \N XREF 39 Genoscope pred transcript MISC \N \N \N
+2920 Genoscope_annotated_gene \N KNOWN 40 Genoscope annotated gene MISC \N \N \N
+2930 Genoscope_pred_translation \N XREF 40 Genoscope pred translation MISC \N \N \N
+2940 Genoscope_ann_transcript \N KNOWN 40 Genoscope annotated transcript MISC \N \N \N
+2950 Genoscope_ann_translation \N KNOWN 40 Genoscope annotated translation MISC \N \N \N
+3300 miRBase \N KNOWNXREF 180 miRBase MISC \N \N \N
+3310 miRBase_predicted \N XREF 1 miRBase predicted MISC \N \N \N
+3400 SGD \N KNOWN 50 SGD MISC \N \N \N
+3500 IPI \N KNOWN 5 IPI MISC \N \N \N
+3800 CCDS \N KNOWN 240 CCDS MISC \N \N \N
+3900 PUBMED \N KNOWN 5 Sequence Publications LIT \N \N \N
+4000 MEDLINE \N KNOWN 5 MEDLINE LIT \N \N \N
+4100 UniGene \N KNOWN 5 UniGene MISC \N \N \N
+4200 RFAM \N XREF 190 RFAM MISC \N \N \N
+4400 Xenbase \N KNOWN 1 Xenbase MISC \N \N \N
+4500 Tiffin \N XREF 1 Tiffin DNA motifs MISC \N \N \N
+4600 OTTG \N XREF 1 Havana gene ALT_GENE \N \N \N
+4610 OTTT \N XREF 1 Havana transcript ALT_TRANS \N \N \N
+4620 OTTP \N XREF 1 Havana translation MISC \N \N \N
+4650 shares_CDS_with \N XREF 1 transcript having same CDS ALT_TRANS \N \N \N
+4670 shares_CDS_with_OTTT \N XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
+4680 shares_CDS_and_UTR_with_OTTT \N XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
+4690 ENSG \N XREF 1 Ensembl gene ALT_GENE \N \N \N
+4700 Medaka \N XREF 1 Medaka Genome Project MISC \N \N \N
+4800 ENST \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4810 ENST_ident \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4820 ENST_CDS \N XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
+4900 TCAG \N KNOWN 75 TCAG Chr 7 Annotation MISC \N \N \N
+5000 Ens_Mm_gene \N XREF 40 Ensembl Mouse Gene MISC \N \N \N
+5010 Ens_Mm_transcript \N XREF 40 Ensembl Mouse Transcript MISC \N \N \N
+5020 Ens_Mm_translation \N XREF 40 Ensembl Mouse Translation MISC \N \N \N
+5100 IMGT_HLA \N KNOWN 7 IMGT/HLA MISC \N \N \N
+5200 Oxford_FGU_Md_gene \N PRED 1 Oxford Ponting Group Monodelphis predictions gene id MISC \N \N \N
+5300 Oxford_FGU_Md_tscript \N PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
+5400 Oxford_FGU_Oa_gene \N PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
+5500 Oxford_FGU_Oa_tscript \N PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
+5700 Ens_Cf_gene \N XREF 5 Ensembl Dog Gene MISC \N \N \N
+5710 Ens_Cf_transcript \N XREF 5 Ensembl Dog Transcript MISC \N \N \N
+5720 Ens_Cf_translation \N XREF 5 Ensembl Dog Translation MISC \N \N \N
+5800 Ens_Dr_gene \N XREF 5 Ensembl Zebrafish Gene MISC \N \N \N
+5810 Ens_Dr_transcript \N XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
+5820 Ens_Dr_translation \N XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
+5900 Ens_Md_gene \N XREF 5 Ensembl Monodelphis Gene MISC \N \N \N
+5901 Ens_Md_transcript \N XREF 5 Ensembl Monodelphis Transcript MISC \N \N \N
+6100 Havana_gene \N XREF 100 Havana gene ID MISC \N \N \N
+6200 Ens_Rn_gene \N XREF 5 Ensembl Rat Gene MISC \N \N \N
+6300 Ens_Ol_gene \N XREF 5 Ensembl Medaka Gene MISC \N \N \N
+6400 Ens_Gg_gene \N XREF 40 Ensembl Chicken Gene MISC \N \N \N
+6410 Ens_Gg_transcript \N XREF 40 Ensembl Chicken Transcript MISC \N \N \N
+6420 Ens_Gg_translation \N XREF 40 Ensembl Chicken Translation MISC \N \N \N
+6500 IMCB_Tr_gene \N XREF 40 IMCB Fugu Gene MISC \N \N \N
+6600 Ens_Ag_gene \N XREF 5 Ensembl Mosquito Gene MISC \N \N \N
+6630 Ens_Am_gene \N XREF 5 Ensembl Bee Gene MISC \N \N \N
+6660 Ens_Ce_gene \N XREF 5 Ensembl Worm Gene MISC \N \N \N
+6690 Ens_Dm_gene \N XREF 5 Ensembl FruitFly Gene MISC \N \N \N
+6720 Ens_Fr_gene \N XREF 5 Ensembl Fugu Gene MISC \N \N \N
+6750 Ens_Pt_gene \N XREF 5 Ensembl Chimpanzee Gene MISC \N \N \N
+6810 Ens_Tn_gene \N XREF 5 Ensembl PufferFish Gene MISC \N \N \N
+6820 Ens_Tr_transcript \N XREF 40 Ensembl Fugu Transcript MISC \N \N \N
+6900 Ens_Ga_translation \N XREF 5 Ensembl Stickleback Translation MISC \N \N \N
+7120 Ens_Aa_translation \N XREF 40 Ensembl Aedes Translation MISC \N \N \N
+7159 AedesGenBank \N PRED 30 Aedes GenBank MISC \N \N \N
+7160 Aedes_ManualAnnotation \N PRED 30 Aedes ManualAnnotation MISC \N \N \N
+7170 Ixodes_ManualAnnotation \N PRED 30 Ixodes ManualAnnotation MISC \N \N \N
+7180 VB_Community_Annotation 1 KNOWN 50 VB Community Annotation MISC \N \N \N
+7200 IMGT/LIGM_DB \N XREF 10 IMGT/LIGM-DB MISC \N \N \N
+7201 IMGT/GENE_DB \N KNOWN 40 IMGT/GENE-DB MISC \N \N \N
+7300 Ens_Mg_transcript \N XREF 40 Ensembl Turkey Transcript MISC \N \N \N
+7400 Ens_Tg_transcript \N XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
+7500 Ens_St_transcript \N XREF 40 Ensembl Squirrel Transcript MISC \N \N \N
+7600 Ens_Fc_transcript \N XREF 40 Ensembl Cat Transcript MISC \N \N \N
+7620 Ens_Fc_translation \N XREF 40 Ensembl Cat Translation MISC \N \N \N
+8000 Vega_mouse_transcript \N XREF 5 Vega mouse transcript MISC \N \N \N
+8100 Platypus_olfactory_receptor \N XREF 40 Platypus olfactory receptor gene MISC \N \N \N
+8200 PRF \N XREF 5 PRF MISC \N \N \N
+8300 PIR \N XREF 5 PIR MISC \N \N \N
+8400 TetNig_cdna \N XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
+8500 GasAcu_cdna \N XREF 40 Stickleback cDNA MISC \N \N \N
+8600 OrnAna_454_cdna \N XREF 40 Platypus 454 cDNA MISC \N \N \N
+8700 TakRub_cdna \N XREF 40 Takifugu cDNA MISC \N \N \N
+8800 CioInt_est \N XREF 40 Ciona intestinalis EST MISC \N \N \N
+8900 CioInt_cdna \N XREF 40 Ciona intestinalis cDNA MISC \N \N \N
+9000 CaeEle_est \N XREF 40 C Elegans EST MISC \N \N \N
+9100 XenTro_Gurdon_EST \N XREF 40 Xenopus Gurdon EST Clusters MISC \N \N \N
+9110 XenTro_cdna \N XREF 40 Xenopus Tropicalis cDNA MISC \N \N \N
+9120 XenLae_cdna \N XREF 40 Xenopus Laevis cDNA MISC \N \N \N
+9200 TakRub_est \N XREF 40 Takifugu EST MISC \N \N \N
+9210 TakRub_annotation \N XREF 40 Takifugu gene annotation MISC \N \N \N
+9220 TakRub_seleno_annotation \N XREF 40 Takifugu selenoprotein annotation MISC \N \N \N
+9400 TetNig_mouse_econtig \N XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
+9410 TetNig_fugu_econtig \N XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
+9420 TetNig_human_econtig \N XREF 40 Genoscope human exofish econtig MISC \N \N \N
+9430 TetNig_human_IPI_econtig \N XREF 40 Genoscope human IPI exofish econtig MISC \N \N \N
+9440 TetNig_mouse_IPI_econtig \N XREF 40 Genoscope mouse IPI exofish econtig MISC \N \N \N
+9450 TetNig_rat_econtig \N XREF 40 Genoscope rat exofish econtig MISC \N \N \N
+9460 TetNig_chick_econtig \N XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
+9500 OryLat_est \N XREF 40 Medaka EST MISC \N \N \N
+9600 Trace_archive \N XREF 40 Trace Archive id MISC \N \N \N
+9700 CioSav_est \N XREF 40 Ciona savignyi EST MISC \N \N \N
+9800 kyotograil_2004 \N PRED 30 Ciona intestinalis Kyotograil 2004 predictions MISC \N \N \N
+9900 kyotograil_2005 \N PRED 30 Ciona intestinalis Kyotograil 2005 predictions MISC \N \N \N
+9950 Kyoto_University \N KNOWN 5 Kyoto University MISC \N \N \N
+10000 wormbase_id \N XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
+10100 EPD \N KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
+10200 GPCR \N KNOWNXREF 5 The G protein-coupled receptor database MISC \N \N \N
+10300 MEROPS \N KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
+10500 TransFac \N KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
+10600 modCB_gene \N KNOWNXREF 5 Caenorhabditis briggsae, InParanoid model organism database MISC \N \N \N
+10700 modCE_gene \N KNOWNXREF 5 Caenorhabditis elegans, InParanoid model organism database MISC \N \N \N
+10800 modDD_gene \N KNOWNXREF 5 Dictyostelium discoideum, InParanoid model organism database MISC \N \N \N
+10900 GI \N XREF 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC \N \N \N
+11000 UCSC \N KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
+11100 Culex_ncRNA \N XREF 70 Culex ncRNAs MISC \N \N \N
+12300 HGNC_curated_gene \N KNOWNXREF 5 HGNC (curated) MISC \N \N \N
+12305 HGNC_automatic_gene \N KNOWNXREF 5 HGNC (automatic) MISC \N \N \N
+12310 Clone_based_vega_gene \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12315 Clone_based_ensembl_gene \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12400 HGNC_curated_transcript \N KNOWNXREF 300 HGNC (curated) MISC \N \N \N
+12405 HGNC_automatic_transcript \N KNOWNXREF 290 HGNC (automatic) MISC \N \N \N
+12410 Clone_based_vega_transcript \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12415 Clone_based_ensembl_transcript \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12500 DBASS3 \N XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
+12505 DBASS5 \N XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
+12510 HPA \N XREF 50 Human Protein Atlas MISC \N \N \N
+12550 MGI_curated_gene \N KNOWNXREF 5 MGI (curated) MISC \N \N \N
+12555 MGI_automatic_gene \N KNOWNXREF 5 MGI (automatic) MISC \N \N \N
+12560 MGI_curated_transcript \N KNOWNXREF 140 MGI (curated) MISC \N \N \N
+12565 MGI_automatic_transcript \N KNOWNXREF 279 MGI (automatic) MISC \N \N \N
+12600 WikiGene \N XREF 50 WikiGene MISC \N \N \N
+12601 Tgut_symbol \N KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
+12610 Fantom \N XREF 50 Fantom MISC \N \N \N
+12620 Duck_consortium \N XREF 0 Duck consortium MISC \N \N \N
+12630 BGI_duck_transcriptome \N XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
+12700 goslim_goa \N XREF 5 GOSlim GOA MISC \N \N \N
+12701 goslim_generic \N XREF 5 GOSlim Generic MISC \N \N \N
+12710 WTSI_gorilla_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
+12720 WTSI_zebrafish_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC \N \N \N
+20005 UniParc \N KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
+20008 BRENDA \N KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
+20009 BioCyc \N KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
+20010 BuruList \N KNOWNXREF 0 BuruList PRIMARY_DB_SYNONYM \N \N \N
+20013 EchoBASE \N KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
+20014 EcoGene \N KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
+20017 GeneDB_Spombe \N KNOWNXREF 0 GeneDB_Spombe PRIMARY_DB_SYNONYM \N \N \N
+20025 Leproma \N KNOWNXREF 0 Leproma PRIMARY_DB_SYNONYM \N \N \N
+20031 2DBase_Ecoli \N KNOWNXREF 0 2DBase-Ecoli PRIMARY_DB_SYNONYM \N \N \N
+20038 SagaList \N KNOWNXREF 0 SagaList PRIMARY_DB_SYNONYM \N \N \N
+20040 SubtiList \N KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
+20042 TIGR \N KNOWNXREF 0 TIGR PRIMARY_DB_SYNONYM \N \N \N
+20043 TubercuList \N KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
+20046 ArrayExpress \N XREF 0 Expression Atlas MISC \N \N \N
+20050 GermOnline \N KNOWNXREF 0 GermOnline PRIMARY_DB_SYNONYM \N \N \N
+20059 DIP \N KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
+20061 DisProt \N KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
+20062 DrugBank \N KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
+20065 GlycoSuiteDB \N KNOWNXREF 0 GlycoSuiteDB PRIMARY_DB_SYNONYM \N \N \N
+20066 HAMAP \N KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
+20067 HOGENOM \N KNOWNXREF 0 HOGENOM PRIMARY_DB_SYNONYM \N \N \N
+20071 HSSP \N KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
+20072 IntAct \N KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
+20074 KEGG \N KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
+20078 PDBsum \N KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
+20082 PeroxiBase \N KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
+20083 PhosSite \N KNOWNXREF 0 PhosSite PRIMARY_DB_SYNONYM \N \N \N
+20084 PptaseDB \N KNOWNXREF 0 PptaseDB PRIMARY_DB_SYNONYM \N \N \N
+20085 REBASE \N KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
+20088 Reactome \N KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
+20090 SWISS_2DPAGE \N KNOWNXREF 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM \N \N \N
+20097 RegulonDb_Transcript \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20099 RegulonDb_Gene \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20101 IntEnz \N KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
+20102 ArrayExpressExperiment \N XREF 0 ArrayExpressExperiment MISC \N \N \N
+20200 EMBLBANK_GENE \N KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20201 GeneDB_SPombe_transcript \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20202 EBACTERIA_GENE \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20203 EBACTERIA_TRANSCRIPT \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20204 EPROTIST_GENE \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20205 EPROTIST_TRANSCRIPT \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20207 EFUNGI_GENE \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20208 EFUNGI_TRANSCRIPT \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20209 EMBLBANK_TRANSCRIPT \N KNOWNXREF 115 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20210 GeneDB_SPombe_gene \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20214 phatr_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20215 phatr_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20216 phatr_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20217 phatr_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20218 phatr_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20219 phatr_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20220 thaps_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20221 thaps_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20222 thaps_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20223 thaps_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20225 thaps_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20226 thaps_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20227 Diatom_EST_Cluster \N XREF 0 ENS EST Cluster (Diatom ESTDB) MISC \N \N \N
+20228 CADRE_Afum_A1163 \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20301 RNAMMER \N KNOWNXREF 0 RNAmmer MISC \N \N \N
+20302 TRNASCAN_SE \N KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
+20303 dictyBase \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20304 dictyBase_gene \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20305 dictyBase_transcript \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20306 ASPGD \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20307 ASPGD_GENE \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20308 ASPGD_TRANSCRIPT \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20309 CADRE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20310 CADRE_GENE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20311 CADRE_TRANSCRIPT \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20312 SGD_GENE \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+20313 SGD_TRANSCRIPT \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+20314 BROAD_PUCCINIA_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20315 BROAD_PUCCINIA_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20316 BROAD_PUCCINIA 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20317 phyra_jgi_v1.1 1.1 KNOWNXREF 0 JGI ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20318 phyra_jgi_v1.1_gene 1.1 KNOWNXREF 0 JGI Gene ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20319 phyra_jgi_v1.1_transcript 1.1 KNOWNXREF 0 JGI transcript ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20320 physo1_jgi_v1.1 1.1 KNOWNXREF 0 JGI ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20321 physo1_jgi_v1.1_gene 1.1 KNOWNXREF 0 JGI Gene ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20322 physo1_jgi_v1.1_transcript 1.1 KNOWNXREF 0 JGI transcript ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
+20323 BROAD_P_infestans_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20324 BROAD_P_infestans_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20325 BROAD_P_infestans 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20326 BROAD_M_oryzae_GENE 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20327 BROAD_M_oryzae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20328 BROAD_M_oryzae 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20329 triad_jgi_v1.0_gene 1 KNOWNXREF 0 JGI Gene ID (JGI Triad 1.0) PRIMARY_DB_SYNONYM \N \N \N
+20330 triad_jgi_v1.0_transcript 1 KNOWNXREF 0 JGI Transcript ID (JGI Triad 1.0) PRIMARY_DB_SYNONYM \N \N \N
+20331 triad_jgi_v1.0 1 KNOWNXREF 0 JGI ID (JGI Triad 1.0) MISC \N \N \N
+20332 GeneDB_GENE 1 KNOWNXREF 0 GeneDB Gene ID PRIMARY_DB_SYNONYM \N \N \N
+20333 GeneDB_TRANSCRIPT 1 KNOWNXREF 0 GeneDB Transcript ID PRIMARY_DB_SYNONYM \N \N \N
+20334 SCHISTODB 1 KNOWNXREF 0 SchistoDB MISC \N \N \N
+20335 SCHISTODB_GENE 1 KNOWNXREF 0 SchistoDB PRIMARY_DB_SYNONYM \N \N \N
+20336 SCHISTODB_TRANSCRIPT 1 KNOWNXREF 0 SchistoDB PRIMARY_DB_SYNONYM \N \N \N
+20337 BROAD_F_oxysporum 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20338 BROAD_F_oxysporum_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20339 BROAD_F_oxysporum_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20340 BROAD_G_zeae 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20341 BROAD_G_zeae_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20342 BROAD_G_zeae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20343 BROAD_G_moniliformis 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20344 BROAD_G_moniliformis_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20345 BROAD_G_moniliformis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20346 GeneDB_TRANSLATION 1 KNOWNXREF 0 GeneDB Translation ID PRIMARY_DB_SYNONYM \N \N \N
+20347 PGD 1 KNOWNXREF 0 Pythium genome database MISC \N \N \N
+20348 PGD_GENE 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
+20349 PGD_TRANSCRIPT 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
+20350 RegulonDb_Operon \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20351 BROAD_N_crassa_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20352 BROAD_N_crassa_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20353 BROAD_N_crassa 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20354 BROAD_U_maydis 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20355 BROAD_U_maydis_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20356 BROAD_U_maydis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20357 BROAD_P_triticina 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
+20358 BROAD_P_triticina_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20359 BROAD_P_triticina_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20360 SpBase 1 KNOWNXREF 0 SpBase MISC \N \N \N
+20361 PHIbase 3.2 XREF 50 PHI-base MISC \N \N \N
+20362 necha_jgi_v2.0_gene 2 KNOWNXREF 0 Nectria JGI gene PRIMARY_DB_SYNONYM \N \N \N
+20363 necha_jgi_v2.0_transcript 2 KNOWNXREF 0 Nectria JGI transcript PRIMARY_DB_SYNONYM \N \N \N
+20364 necha_jgi_v2.0 2 KNOWNXREF 0 Nectria JGI MISC \N \N \N
+20365 tuber_genoscope_gene 1 KNOWNXREF 0 Tuber Genome Browser PRIMARY_DB_SYNONYM \N \N \N
+20366 tuber_genoscope_transcript 2 KNOWNXREF 0 Tuber Genome Browser PRIMARY_DB_SYNONYM \N \N \N
+20367 tuber_genoscope 2 KNOWNXREF 0 Tuber Genome Browser MISC \N \N \N
+20368 Mycgr3_jgi_v2.0_gene 2 KNOWNXREF 0 Mycosphaerella JGI gene PRIMARY_DB_SYNONYM \N \N \N
+20369 Mycgr3_jgi_v2.0_transcript 2 KNOWNXREF 0 Mycosphaerella JGI transcript PRIMARY_DB_SYNONYM \N \N \N
+20370 Mycgr3_jgi_v2.0 2 KNOWNXREF 0 Mycosphaerella JGI MISC \N \N \N
+20371 BROAD_P_NODORUM 1 KNOWNXREF 0 Broad Phaeosphaeria nodorum MISC \N \N \N
+20372 BROAD_P_NODORUM_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20373 BROAD_P_NODORUM_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20375 PomBase 1 KNOWN 0 PomBase MISC \N \N \N
+20376 PomBase_GENE 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
+20377 PomBase_TRANSCRIPT \N KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
+20378 PomBase_TRANSLATION 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
+20379 SPO \N KNOWNXREF 0 SPO ID MISC \N \N \N
+20380 CBS \N KNOWNXREF 0 CBS Server MISC \N \N \N
+20381 COG \N KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
+20382 CGD \N KNOWN 0 Candida Genome Database MISC \N \N \N
+20383 ProSite \N XREF 0 ProSite ID MISC \N \N \N
+20385 SMART \N XREF 0 SMART ID MISC \N \N \N
+20386 SPD \N KNOWNXREF 0 SPD ID MISC \N \N \N
+20387 KOG \N KNOWNXREF 0 KOG ID MISC \N \N \N
+20388 PBO \N KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
+20389 FYPO \N KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
+20390 MOD \N KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
+20391 AGD_GENE 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
+20392 AGD_TRANSCRIPT 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
+20393 AGD 1 KNOWNXREF 0 Ashbya Genome Database MISC \N \N \N
+20394 FYPO_GENE 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
+20395 FYPO_TRANSCRIPT 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
+50000 BGI_EST_Cluster \N XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
+50005 EC_NUMBER \N XREF 0 Enzyme EC Number MISC \N \N \N
+50010 FSTs \N XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
+50015 gene_name \N KNOWNXREF 0 Gene Name MISC \N \N \N
+50020 Gramene_Pathway \N XREF 0 Gramene Pathway MISC \N \N \N
+50030 Gramene_GenesDB \N KNOWNXREF 100 Gramene Curated Gene MISC \N \N \N
+50035 Gramene_MarkersDB \N XREF 0 Gramene MISC \N \N \N
+50040 Gramene_MarkersDB_mRNA \N XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
+50050 Gramene_MarkersDB_EST \N XREF 0 GenBank EST (Gramene) MISC \N \N \N
+50060 IRGSP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50065 KOME \N KNOWNXREF 0 Full Length cDNA (KOME) MISC \N \N \N
+50070 miRNA_Accession \N XREF 0 miRNA miRBase accession MISC \N \N \N
+50080 miRNA_Registry \N XREF 1 miRNA Registry MISC \N \N \N
+50090 NASC_GENE_ID \N XREF 1 NASC Gene ID MISC \N \N \N
+50100 NASC_TRANSCRIPT_ID \N XREF 1 NASC Transcript ID MISC \N \N \N
+50110 PlantGDB_PUT \N XREF 1 PlantGDB Transcript MISC \N \N \N
+50120 RAP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50130 siRNA_Sunkar \N XREF 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC \N \N \N
+50140 TIGR_LOCUS \N XREF 1 MSU/TIGR Locus MISC \N \N \N
+50150 TIGR_LOCUS_MODEL \N XREF 0 MSU/TIGR Locus (Model) MISC \N \N \N
+50160 TAIR_LOCUS \N XREF 8 TAIR MISC \N \N \N
+50170 TAIR_LOCUS_MODEL \N XREF 8 TAIR Locus (Model) MISC \N \N \N
+50180 TIGR_GeneIndex \N XREF 0 Gene Index MISC \N \N \N
+50185 TO \N XREF 0 Plant Trait Ontology MISC \N \N \N
+50190 PO \N XREF 0 Plant Structure Ontology MISC \N \N \N
+50195 PO_to_gene \N XREF 0 Plant Structure Ontology MISC \N \N \N
+50196 GO_to_gene \N XREF 0 Gene Ontology MISC \N \N \N
+50200 GRO \N XREF 0 Plant Growth Stage MISC \N \N \N
+50510 AFFY_RICE \N XREF 1 Affymx GeneChip Rice ARRAY \N \N \N
+50520 AFFY_ATH1 \N XREF 1 Affymx GeneChip ATH1 ARRAY \N \N \N
+50530 AFFY_Vitis_Vinifera \N XREF 1 Affymx GeneChip Vitis vinifera ARRAY \N \N \N
+50540 AFFY_Poplar \N XREF 1 Affymx GeneChip Poplar ARRAY \N \N \N
+50541 LRG \N KNOWN 10 Locus Reference Genomic MISC \N \N \N
+50542 ENS_LRG_gene \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50543 ENS_LRG_transcript \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50600 IKMCs_KOs \N XREF 10 International Knockout Mouse Consortium Knockouts MISC \N \N Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse
+50601 IKMCs_ES_cells_available \N XREF 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC \N \N Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (ES cells available)
+50602 IKMCs_Mice_available \N XREF 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC \N \N Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (Mice available)
+50603 IKMCs_No_products_available_yet \N XREF 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC \N \N Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (No products available yet)
+50604 IKMCs_Vector_available \N XREF 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC \N \N Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (Vector available)
+50605 RFAM_gene_name \N KNOWNXREF 5 RFAM gene name MISC \N \N gene name from RFAM
+50606 miRBase_gene_name \N KNOWNXREF 5 miRBase gene name MISC \N \N gene name from miRBase
+50607 miRBase_trans_name \N KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
+50608 RFAM_trans_name \N KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
+50609 HGNC_trans_name \N KNOWNXREF 5 HGNC transcript name MISC \N \N transcript name from HGNC
+50610 MGI_trans_name \N KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
+50611 ZFIN_ID_trans_name \N KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
+50612 LampreyGenomeProject \N KNOWN 1 Lamprey Genome Project MISC \N \N \N
+50620 Illumina_Bodymap_transcriptome \N XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
+50621 Uniprot_gn \N KNOWN 116 UniProtKB Gene Name MISC \N \N \N
+50622 GGSC \N KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
+50623 Broad Institute \N KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
+50624 PFAM \N XREF 0 PFAM MISC \N \N Pfam from Vega
+50625 SGSC \N KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
+50626 RIKEN \N KNOWN 5 Riken Institute MISC \N \N \N
+50627 SHSC \N KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
+50628 PFAM 22 XREF 0 PFAM MISC \N \N Pfam release 22, from Vega
+50629 PFAM 23 XREF 0 PFAM MISC \N \N Pfam release 23, from Vega
+50630 PFAM 24 XREF 0 PFAM MISC \N \N Pfam release 24, from Vega
+50631 PFAM 25 XREF 0 PFAM MISC \N \N Pfam release 25, from Vega
+50632 PFAM 26 XREF 0 PFAM MISC \N \N Pfam release 26, from Vega
+50633 GRC_primary_assembly \N XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
+50634 Ens_Ga_gene \N XREF 5 Ensembl Stickleback Gene MISC \N \N \N
+50635 Ens_Ga_transcript \N XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
+50637 CSAC \N KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
+50640 PomBase_Interaction_GENETIC 1 KNOWNXREF 5 PomBase Interaction Genetic MISC \N \N \N
+50641 PomBase_Interaction_PHYSICAL 1 KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
+50642 PomBase_Gene_Name 1 KNOWNXREF 5 PomBase Gene Name MISC \N \N \N
+50643 PomBase_Systematic_ID 1 KNOWNXREF 5 PomBase Systematic ID MISC \N \N \N
+50644 PomBase_Ortholog 1 KNOWNXREF 5 Orthologous Gene MISC \N \N \N
+50645 Ens_Ss_translation \N XREF 5 Ensembl Pig Translation MISC \N \N \N
+50646 Psinensis_sequencing_consortium \N KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
+50647 BROAD_Magnaporthe_DB 1 KNOWNXREF 0 Magnaporthe comparative DB MISC \N \N Broad Institute Magnaporthe comparative Database
+50648 BROAD_Magnaporthe_DB_GENE 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
+50649 BROAD_Magnaporthe_DB_TRANSCRIPT 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
+50650 BGI Shenzhen \N KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
+50651 ICGSC \N KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
+50652 SGD_TRANSLATION 1 KNOWNXREF 0 SGD MISC \N \N SGD Mapping attached to S.cerevisiae translations objects so we can attach GO dependant annotations at the translation level as well.
+50653 WashingtonUniversity \N KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
+50654 BDGP_cDNA 1 KNOWN 50 Fly cDNA MISC \N \N cDNA from the Berkeley Drosophila Genome Project
+50655 BDGP_cDNA_Gold_Collection 1 KNOWN 50 Fly gold cDNA MISC \N \N Gold Collection cDNA from the Berkeley Drosophila Genome Project
+50656 Ens_Tg_translation \N KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
+50657 BudgerigarGenomeProject \N KNOWN 0 Budgerigar Genome Project MISC \N \N Melopsittacus undulatus sequenced by Washington University School of Medicine
+50658 ToxoDB 1 KNOWNXREF 1 ToxoDB PRIMARY_DB_SYNONYM \N \N Toxoplasma Genomic Resource Database.
+50659 Orphanet \N XREF 50 Orphanet MISC \N \N Database of rare diseases and orphan drugs
+50660 SO 1 KNOWNXREF 0 Sequence Ontology MISC \N \N Sequence Ontology
+50661 BRAD_GENE 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
+50662 BRAD_TRANSCRIPT 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
+50663 Quick_Go \N KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
+50664 Quick_Go_Evidence \N KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
+50665 Painted_Turtle_Consortium 3.0.1 KNOWN 5 International Painted Turtle Genome Sequencing Consortium MISC \N \N http://www.ncbi.nlm.nih.gov/genome/assembly/326468/
+50666 IGDBCAS-v1.4_GENE 1.4 KNOWN 1 IGDBCAS v1.4 Gene MISC \N \N \N
+50667 IGDBCAS-v1.4_TRANSCRIPT 1.4 KNOWN 1 IGDBCAS v1.4 Transcript MISC \N \N \N
+50668 JGI_GENE 1 XREF 1 JGI Gene MISC \N \N gene ID/NAME in the JGI gff3 file
+50669 JGI_TRANSCRIPT 1 XREF 1 JGI Transcript MISC \N \N transcript/mRNA ID/NAME in the JGI gff3 file
+50670 ITAG_GENE ITAG_pre2.3 KNOWNXREF 0 ITAG pre2.3 Gene MISC \N \N \N
+50671 ITAG_TRANSCRIPT ITAG_pre2.3 KNOWNXREF 1 ITAG pre2.3 Transcript MISC \N \N \N
+50672 IRGSPv1_GENE 1 KNOWNXREF 1 IRGSP v1 Gene MISC \N \N \N
+50673 IRGSPv1_TRANSCRIPT 1 KNOWNXREF 1 IRGSP v1 Transcript MISC \N \N \N
+50674 Ens_Lc_gene \N XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
+50675 Ens_Lc_transcript \N XREF 170 Ensembl Coelacanth Transcript MISC \N \N \N
+50676 Ens_Lc_translation \N XREF 5 Ensembl Coelacanth Translation MISC \N \N \N
+50677 RGSC \N KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
+50678 BROAD_coelacanth_transcriptome \N XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
+50679 Ens_Ac_translation \N XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
+50680 Ens_Ac_gene \N XREF 40 Ensembl Anole Lizard Gene MISC \N \N \N
+50681 Ens_Ac_transcript \N XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
+50682 BGI_Gene 1 XREF 50 BGI_2005_indica_Gene MISC \N \N BGI gene identifier
+50683 GeneIndex 1 XREF 50 GeneIndex MISC \N \N \N
+50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms.
\
+More information in there:
\
+http://www.gramene.org/plant_ontology/ontology_browse.html#eo
+50685 Ens_Rn_transcript \N XREF 5 Ensembl Rat Transcript MISC \N \N \N
+50686 Ens_Rn_translation \N XREF 5 Ensembl Rat Translation MISC \N \N \N
+50687 Uppsala University \N KNOWN 5 Uppsala University MISC \N \N \N
+50688 GenBank 1 XREF 1 GenBank MISC \N \N GenBank identifier
+50689 MaizeGDB_GenBank 1 XREF 1 MaizeGDB_GenBank MISC \N \N GenBank identifiers for Maize Genome DB entries.
+50690 RefSeq_gene_name \N KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
+50691 SGN 1 KNOWNXREF 1 Sol Genomics Network MISC \N \N \N
+50692 GRC_alignment_import \N XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
+50693 BROAD_monodelphis_transcriptome \N XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
+50694 SIB_mondelphis_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
+50695 SIB_platypus_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
+50696 SIB_orangutan_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
+50697 NCBI_TAXONOMY 1 KNOWNXREF 1 NCBI species MISC \N \N Organism listed in NCBI
+50698 PHI 1 KNOWNXREF 1 PHI-base accession MISC \N \N Parasite-host interaction identifiers from PHI-base
+50700 AnoXcel 2 KNOWN 50 AnoXcel MISC \N \N VectorBase xref.
+50701 PGSC_GENE 1 XREF 1 PGSC MISC \N \N Potato Genome Sequencing Consortium database
+50702 PHYTOZOME_GMAX_GENE 1.1 XREF 1 Phytozome MISC \N \N Phytozome Gmax
+50703 Uniprot_gn_trans_name \N KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
+50705 Uniprot_gn_gene_name \N KNOWNXREF 5 UniProt gene name MISC \N \N gene name from UniProt
+50707 Ensembl_Bam2Genes_intron \N PRED 5 Intron identified by Ensembl RNASeq pipeline MISC \N \N Ensembl_Bam2Genes_intron are the introns indentified at the bam2genes stage in the Ensembl RNAseq pipeline. They are stored as Clusters in the dna_align_feature table.
+50708 GMGC_GENE 1 KNOWNXREF 1 GMGC PRIMARY_DB_SYNONYM \N \N Global Musa Genomics Consortium gene cross-references
+50709 tamu_vibs \N KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
+50710 INSDC 0 KNOWNXREF 5 International Nucleotide Sequence Database Collaboration MISC INSDC \N This external_db_id was initially made for use in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The INSDC accession is stored as a synonym.
+50711 ISGC \N KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
+50712 PO_to_transcript 1 KNOWNXREF 1 PO MISC \N \N Plants Ontology terms attached to transcripts
+50713 TAIR_SYMBOL 10 KNOWN 60 TAIR Gene Name PRIMARY_DB_SYNONYM \N \N TAIR gene names
+50714 GO_to_transcript 1 KNOWNXREF 1 GO MISC \N \N GO Terms attached to transcripts
+50715 TIGR_ID 1 XREF 1 TIGR Internal ID MISC \N \N cross-references to TIGR internal identifiers, attached to genes.
+50716 TIGR_TRANSCRIPT_ID 1 XREF 1 TIGR Internal ID MISC \N \N cross-references to TIGR internal identifiers, attached to transcripts
+50717 GOA 1 KNOWNXREF 1 GOA MISC \N \N GOA xrefs (to UniProt identifiers)
+50718 ENA_GENE 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source gene model when importing from ENA.
+50719 ENA_TRANSCRIPT 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source transcript model when importing from ENA.
+50720 LGBPratt_EST_Cluster 1 KNOWNXREF 1 LGBPratt_EST_Cluster MISC \N \N \N
+50721 BaylorCollege \N KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
+50722 Rhea 1 KNOWNXREF 1 Rhea MISC \N \N Cross-references to Rhea attached to translation objects
+50723 Ens_Bt_translation \N XREF 5 Ensembl Cow Translation MISC \N \N \N
+50724 RegulonDB_GENE 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to gene objects
+50725 RegulonDB_OPERON 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to operon objects
+50726 ENA_FEATURE_GENE 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the gene has been inferred, when loading a genome from ENA records.
+50727 ENA_FEATURE_TRANSCRIPT 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the transcript has been inferred, when loading a genome from ENA records.
+50728 ENA_FEATURE_PROTEIN 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the translation has been inferred, when loading a genome from ENA records.
+50729 RefSeq_import \N KNOWN 240 RefSeq_import MISC \N \N \N
+50730 AGP \N KNOWN 5 Anolis Genome Project MISC \N \N \N
+50731 Turkey Genome Consortium \N KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
+50732 Yutaka_Satou_Kyoto_University \N KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
+50733 Chicken_Genome_Consortium \N KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
+50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifier MISC \N \N TAIR identifier to link to Ensembl Translation entities.
\
+The main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translation objects.
+50735 AGI_GENE 1 XREF 1 AGI Gene MISC \N \N annotation provided by Arizona Genome Institute
+50736 AGI_TRANSCRIPT 1 XREF 1 AGI Transcript MISC \N \N annotation provided by Arizona Genome Institute
+50737 CGNC \N KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+50738 MetaCyc 1 KNOWNXREF 1 MetaCyc MISC \N \N MetaCyc database of metabolic pathways
+50739 PHIP 1 KNOWNXREF 1 PHI-base phenotype ontology MISC \N \N PHI-base phenotype ontology for genes proven to affect the outcome of pathogen-host interactions
+50740 PHIE 1 KNOWNXREF 1 PHI-base condition ontology MISC \N \N PHI-base experimental evidence ontology for genes proven to affect the outcome of pathogen-host interactions
+50741 dbSNP \N XREF 101 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
+50742 PubMedCentral \N KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
+50743 PFAM 27 XREF 0 PFAM MISC \N \N Pfam release 27, from Vega
+50744 EntrezGene_trans_name \N KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
+50745 BROAD_M_violaceum 1 KNOWNXREF 0 Broad Institute MISC \N \N Broad Institute Microbotryum violaceum Database
+50746 BROAD_M_violaceum_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
+50747 BROAD_M_violaceum_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
+50748 Ensembl_Plants 1 XREF 1 Ensembl Plants ENSEMBL \N \N Ensembl Plants identifiers serving GO projections from a reference species to other plants species.
+50749 ChEMBL \N KNOWNXREF 5 ChEMBL MISC \N \N ChEMBL external references imported via Uniprot mappings
+50750 IBSC 1 KNOWNXREF 50 IBSC Gene ID MISC \N \N International Barley Sequencing Consortium gene identifier
+50751 PharmGKB \N XREF 0 Pharmacogenomics Knowledgebase MISC \N \N \N
+50752 PRIDE \N XREF 0 PRIDE MISC \N \N \N
+50753 LegioList \N XREF 0 LegioList MISC \N \N Database dedicated to the analysis of the genomes of Legionella
+50755 BindingDB \N XREF 0 BindingDB MISC \N \N BindingDB is a public, web-accessible database of measured binding affinities
+50756 STRING \N XREF 0 STRING MISC \N \N STRING - Known and Predicted Protein-Protein Interactions
+50757 UniPathway \N XREF 0 UniPathway MISC \N \N UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions.
+50759 SWISS_MODEL \N XREF 0 SWISS-MODEL MISC \N \N The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
+50760 MypuList \N XREF 0 MypuList MISC \N \N A database dedicated to the analysis of the genome of Mycoplasma pulmoni
+50761 ListiList \N XREF 0 ListiList MISC \N \N A database dedicated to the analysis of the genomes of the food-borne pathogen, Listeria monocytogenes, and its non-pathogenic relative, Listeria innocua
+50762 CYGD \N XREF 0 CYGD MISC \N \N The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae.
+50763 PhotoList \N XREF 0 PhotoList MISC \N \N A database dedicated to the analysis of the genome of Photorhabdus luminescens
+50770 PseudoCAP \N XREF 0 Pseudomonas Genome Database MISC \N \N The Pseudomonas Genome database has been a resource for peer-reviewed, continually-updated annotations for the Pseudomonas aeruginosa PAO1 reference strain's genome and, more recently, comparative analyses of several related Pseudomonas species.
+50771 MINT \N XREF 0 MINT MISC \N \N MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators.
+50772 Ant Genomes Portal \N KNOWNXREF 0 Ant Genomes Portal MISC \N \N \N
+50773 MaizeGDB_GENE 1 KNOWNXREF 50 MaizeGDB PRIMARY_DB_SYNONYM \N \N MaizeGDB reference database for Zea mays genome
+50774 Ens_Mg_gene \N XREF 40 Ensembl Turkey Gene MISC \N \N \N
+50775 Ens_Mg_translation \N XREF 40 Ensembl Turkey Translation MISC \N \N \N
+50776 LNCC \N XREF 30 LNCC MISC \N \N The National Laboratory of Scientific Computation (Laboratorio Nacional de Computacao Cientifica: LNCC), Brazil
+50777 RGD_trans_name \N KNOWNXREF 50 RGD transcript name MISC \N \N transcript name from RGD
+50778 Xenbase_trans_name \N KNOWN 1 Xenbase transcript name MISC \N \N transcript name from Xenbase
+50779 NasoniaBase \N KNOWN 0 NasoniaBase MISC \N \N \N
+50780 wormbase_gseqname \N KNOWN 6 WormBase Gene Sequence-name MISC \N \N \N
+50783 ENSP_ident \N XREF 1 Ensembl translation having exact match with Havana ALT_TRANS \N \N \N
+50782 Sanger \N KNOWN 5 Sanger Wellcome Trust Institute MISC \N \N \N
+50781 TriTryp_pathway_comparison 1 KNOWNXREF 50 TriTryp pathway comparison database MISC \N \N TriTryp pathway comparison database (http://tritrypdb.org/tritrypdb/)
\
+
+50784 Ensembl_Metazoa 1 XREF 1 Ensembl Metazoa ENSEMBL \N \N Ensembl Metazoa identifiers serving GO projections from a reference species to other metazoa species.
+50785 Ens_Mmu_translation \N XREF 40 Ensembl Macaque Translation MISC \N \N \N
+50786 PomBase_GO_AnnotationExtensions \N KNOWN 1 PomBase GO AnnotationExtensions MISC \N \N Specific accession used by PomBase for ontology annoation extensions
+50788 SP_SL \N KNOWN 0 UniProtKB/SwissProt Subcellular Locatisation MISC \N \N UniProt Subcellular Location (http://www.uniprot.org/manual/subcellular_location)
+50789 PR \N KNOWNXREF 0 Protein Ontology MISC \N \N Protein Ontology term (previously PR) - http://pir.georgetown.edu/pro/pro.shtml
+50790 PUBMED_POMBASE \N KNOWN 1 PomBase PubMed ID LIT \N \N PomBase specific publications
+50791 PUBMED_TRANSCRIPT \N KNOWN 0 PUBMED LIT \N \N Publications attached to the transcript
+50792 CL \N KNOWNXREF 0 Cell Type Ontology MISC \N \N Cell type ontology annotations (http://cellontology.org/)
+50793 ChEBI \N KNOWNXREF 0 ChEBI Chemical Database MISC \N \N ChEBI chemical database
+50794 FYPO_EXT \N KNOWNXREF 1 FYPO Extensions MISC \N \N Annotation extension terms for the Fission Yeast Phenotype Ontology (FYPO)
+50795 EcoCyc \N KNOWNXREF 1 EcoCyc MISC \N \N Scientific database for E. coli and a division of MetaCyc (http://ecocyc.org/)
+50796 PATO \N KNOWNXREF 1 Phenotypic Qualities Ontology MISC \N \N http://obofoundry.org/wiki/index.php/PATO:Main_Page
+50797 UniProtKB-KW \N KNOWNXREF 0 UniProtKB Keywords MISC \N \N UniProtKB Keywords for describing UniProt annotations
+50798 PBQ \N KNOWNXREF 0 PomBase Quiescence Ontology MISC \N \N Used in the annotation of quiescent cell phenotypes.
+50799 University of Texas \N KNOWN 5 University of Texas MISC \N \N \N
+50801 KEGG_Enzyme \N XREF 0 KEGG MISC \N \N KEGG pathway and enzyme
+50802 gfbgp \N KNOWN 0 Glanville Fritillary Butterfly Genome Project MISC \N \N \N
+50803 ensembl_internal_synonym \N KNOWNXREF 100 Ensembl internal synonym MISC \N \N \N
+50804 Ensembl_Vertebrates 1 XREF 1 Ensembl Vertebrates ENSEMBL \N \N Vertebrate Ensembl identifier serving GO projections from a reference species to other non-vertebrate species.
+50805 Ens_Tt_translation \N XREF 40 Ensembl Dolphin Translation MISC \N \N \N
+50806 Ens_Tt_gene \N XREF 40 Ensembl Dolphin Gene MISC \N \N \N
+50807 Ens_Tt_transcript \N XREF 40 Ensembl Dolphin Transcript MISC \N \N \N
+50808 DOI \N KNOWN 5 Digital Object Identifier LIT \N \N Digital Object Identifier used to uniquely identify an object such as an electronic document.
diff --git a/modules/t/test-genome-DBs/polyploidy/core/external_synonym.txt b/modules/t/test-genome-DBs/polyploidy/core/external_synonym.txt
new file mode 100644
index 0000000000..121d2389ee
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/external_synonym.txt
@@ -0,0 +1,115 @@
+458168 ycf6
+458170 ndh3
+458210 frxB
+458234 ndh4
+458278 ndh4L
+458292 secX
+458312 ndh2
+458356 ndh5
+458378 ndh1
+458412 ycf10
+458420 ycf5
+458422 ndh2
+460982 Q70LR2
+461056 ALPHA-AMY3
+461062 AMY1
+461069 P20599
+461097 P00836
+461097 P20859
+461107 P00843
+461107 Q33180
+461107 Q9XPT1
+461193 Q4W1G1
+461211 P25411
+461227 P08741
+461228 COI
+461228 COXI
+461234 COII
+461234 COXII
+461243 P93595
+461258 P12362
+461258 Q32438
+461266 COB
+461266 CYTB
+461266 MTCYB
+461336 Q41555
+461358 COMT1
+461361 B8LGB9
+461388 wga20
+461393 Q8L5J9
+461473 AGA.3
+461534 Q43310
+461534 Q9SB25
+461535 TH274
+461582 P02300
+461585 P02308
+461585 P59258
+461588 P02308
+461588 P59258
+461643 HSP26.6
+461654 O49956
+461654 Q99300
+461704 Q4TZQ0
+461704 Q546I0
+461767 P23513
+461824 P58282
+461827 P58282
+461845 O98694
+461849 NAD4
+461869 NAD6
+461898 P12121
+461898 P32973
+461901 Q5K3U9
+461906 P12178
+461906 P56789
+461907 ycf6
+461963 P10794
+461968 P25410
+461974 P19443
+462001 P05169
+462001 P10879
+462001 Q95H57
+462009 P05171
+462009 P09198
+462009 Q95H58
+462009 Q9M3L1
+462017 P04965
+462017 P09448
+462028 P09970
+462042 O47030
+462042 P12166
+462042 P12167
+462042 Q34007
+462054 P12171
+462070 P37260
+462077 P08890
+462077 Q40003
+462084 Q5BHS1
+462084 Q6J542
+462084 Q6L5P2
+462106 Q546N5
+462106 Q5BHS0
+462106 Q6ISY2
+462106 Q6J5P4
+462150 Q7YKX2
+462194 P11535
+462194 P41097
+462214 P12143
+462272 P20283
+462289 Q9TNM0
+462305 P05424
+462323 P10851
+462342 SH6.2
+462342 SHH
+462373 Q9LEB9
+462404 TFIID
+462408 TFIID
+462418 PUR-D1
+462423 PUR-B1
+462455 U2AF65
+462459 UBC1
+462481 O82079
+462481 P03993
+462517 EXT
+462523 P30981
+462523 P30982
diff --git a/modules/t/test-genome-DBs/polyploidy/core/gene.txt b/modules/t/test-genome-DBs/polyploidy/core/gene.txt
new file mode 100644
index 0000000000..8da3211292
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/gene.txt
@@ -0,0 +1,6 @@
+23688 protein_coding 119 3495727 898 1416 -1 \N ensembl NOVEL \N 1 79141 Traes_6DS_3B68FB2E11 1 2014-01-21 14:05:47 2014-01-21 14:05:47
+23830 protein_coding 119 3495727 8829 9015 1 \N ensembl NOVEL \N 1 79459 Traes_6DS_F1A510F0D1 1 2014-01-21 14:05:48 2014-01-21 14:05:48
+24399 protein_coding 119 3495727 1853 2068 1 462285 ensembl KNOWN 30S ribosomal protein S19, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:P60577] 1 80726 Traes_6DS_262C704652 1 2014-01-21 14:05:56 2014-01-21 14:05:56
+37263 protein_coding 119 3495794 323 5415 -1 \N ensembl NOVEL \N 1 116850 Traes_5AL_7256A9F19 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+39717 protein_coding 119 3495644 2408 2611 -1 \N ensembl NOVEL \N 1 123920 Traes_6BS_5FDE5650B 1 2014-01-21 14:18:24 2014-01-21 14:18:24
+40233 protein_coding 119 3495644 2030 2272 -1 \N ensembl NOVEL \N 1 124987 Traes_6BS_48A5D59CE 1 2014-01-21 14:18:30 2014-01-21 14:18:30
diff --git a/modules/t/test-genome-DBs/polyploidy/core/gene_archive.txt b/modules/t/test-genome-DBs/polyploidy/core/gene_archive.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/gene_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/gene_attrib.txt
new file mode 100644
index 0000000000..4c7ec46a33
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/gene_attrib.txt
@@ -0,0 +1,6 @@
+23830 142 32.09
+37263 142 38.66
+23688 142 55.11
+39717 142 41.18
+24399 142 41.20
+40233 142 35.80
diff --git a/modules/t/test-genome-DBs/polyploidy/core/genome_statistics.txt b/modules/t/test-genome-DBs/polyploidy/core/genome_statistics.txt
new file mode 100644
index 0000000000..165d92e36e
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/genome_statistics.txt
@@ -0,0 +1,10 @@
+4 ref_length 4294967295 1 405 2014-11-25 16:03:21
+39 lnoncoding_cnt 14 1 390 2014-11-25 16:03:21
+7 total_length 4294967295 1 406 2014-11-25 16:03:21
+43 PredictionTranscript 39237 1 424 2014-11-25 16:09:37
+15 transcript 111488 1 403 2014-12-02 16:27:20
+40 snoncoding_cnt 10128 1 389 2014-11-25 16:03:21
+38 coding_cnt 99926 1 64 2014-11-25 16:03:21
+44 SNPCount 10960049 1 10 2014-12-02 16:27:20
+42 PredictionTranscript 83160 1 423 2014-11-25 16:09:37
+41 pseudogene_cnt 1420 1 67 2014-11-25 16:03:21
diff --git a/modules/t/test-genome-DBs/polyploidy/core/identity_xref.txt b/modules/t/test-genome-DBs/polyploidy/core/identity_xref.txt
new file mode 100644
index 0000000000..1397e555d9
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/identity_xref.txt
@@ -0,0 +1,2 @@
+3508135 76 100 23 93 1 71 71M 374 \N
+3506965 76 100 23 93 1 71 71M 374 \N
diff --git a/modules/t/test-genome-DBs/polyploidy/core/interpro.txt b/modules/t/test-genome-DBs/polyploidy/core/interpro.txt
new file mode 100644
index 0000000000..381631a41e
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/interpro.txt
@@ -0,0 +1,10218 @@
+IPR000007 3c5nA00
+IPR000007 PF01167
+IPR000007 PR01573
+IPR000008 2.60.40.150
+IPR000008 PF00168
+IPR000008 PR00360
+IPR000008 PS50004
+IPR000008 SM00239
+IPR000008 SSF49562
+IPR000009 PIRSF037309
+IPR000009 PR00600
+IPR000009 PTHR11871
+IPR000010 PF00031
+IPR000010 SM00043
+IPR000011 PR01849
+IPR000014 PF13426
+IPR000014 PS50112
+IPR000014 SM00091
+IPR000014 SSF55785
+IPR000014 TIGR00229
+IPR000022 PF01039
+IPR000023 PF00365
+IPR000023 SSF53784
+IPR000031 3.40.50.7700
+IPR000031 PF00731
+IPR000031 SM01001
+IPR000031 SSF52255
+IPR000031 TIGR01162
+IPR000033 SM00135
+IPR000039 PTHR10934
+IPR000043 MF_00563
+IPR000043 PF05221
+IPR000043 PIRSF001109
+IPR000043 PTHR23420
+IPR000043 SM00996
+IPR000043 TIGR00936
+IPR000047 PR00031
+IPR000048 PF00612
+IPR000048 PS50096
+IPR000048 SM00015
+IPR000049 PS01065
+IPR000054 PD006030
+IPR000054 PF01198
+IPR000054 PTHR10956
+IPR000056 PF00834
+IPR000056 PS01085
+IPR000056 PS01086
+IPR000056 PTHR11749
+IPR000056 TIGR01163
+IPR000058 4.10.1110.10
+IPR000058 PF01428
+IPR000058 PS51039
+IPR000058 SM00154
+IPR000061 PF01805
+IPR000061 PS50128
+IPR000061 SM00648
+IPR000061 SSF109905
+IPR000064 3.90.1720.10
+IPR000070 PF01095
+IPR000073 PF00561
+IPR000073 PF12697
+IPR000073 PR00111
+IPR000077 MF_00629
+IPR000077 PF00832
+IPR000077 PTHR19970
+IPR000086 PF00293
+IPR000086 PS51462
+IPR000089 PF00364
+IPR000089 PS50968
+IPR000092 PF00348
+IPR000092 PS00444
+IPR000092 PS00723
+IPR000095 3.90.810.10
+IPR000095 PF00786
+IPR000095 PS50108
+IPR000095 SM00285
+IPR000101 PF01019
+IPR000101 PR01210
+IPR000101 PTHR11686
+IPR000101 TIGR00066
+IPR000103 PR00469
+IPR000106 PR00719
+IPR000109 PF00854
+IPR000109 PTHR11654
+IPR000111 PF02065
+IPR000111 PS00512
+IPR000114 MF_01342
+IPR000114 PR00060
+IPR000114 PTHR12220
+IPR000114 TIGR01164
+IPR000115 MF_00138
+IPR000115 TIGR00877
+IPR000116 PR00930
+IPR000118 PF00396
+IPR000118 SM00277
+IPR000120 PF01425
+IPR000120 PTHR11895
+IPR000121 PF02896
+IPR000127 PF02134
+IPR000131 MF_00815
+IPR000131 PF00231
+IPR000131 PR00126
+IPR000131 PTHR11693
+IPR000131 TIGR01146
+IPR000132 PS00920
+IPR000132 PS00921
+IPR000133 PF00810
+IPR000133 PR00660
+IPR000133 PS00951
+IPR000133 PS00952
+IPR000133 PTHR10585
+IPR000136 PF01277
+IPR000136 PS00811
+IPR000138 PS01062
+IPR000146 MF_01855
+IPR000146 PF00316
+IPR000146 PIRSF000904
+IPR000146 PTHR11556
+IPR000150 PS01228
+IPR000150 TIGR00099
+IPR000152 PS00010
+IPR000156 PF00638
+IPR000156 PS50196
+IPR000156 SM00160
+IPR000157 3.40.50.10140
+IPR000157 PF13676
+IPR000157 PS50104
+IPR000157 SM00255
+IPR000157 SSF52200
+IPR000158 MF_00909
+IPR000158 PR00423
+IPR000158 TIGR00065
+IPR000163 PR00679
+IPR000163 PTHR23222
+IPR000164 PR00622
+IPR000164 PS00322
+IPR000164 PS00959
+IPR000164 PTHR11426
+IPR000164 SM00428
+IPR000167 PF00257
+IPR000167 PS00315
+IPR000167 PS00823
+IPR000169 PS00139
+IPR000172 PF00732
+IPR000172 PS00623
+IPR000172 PS00624
+IPR000178 MF_00100_B
+IPR000178 TIGR00487
+IPR000181 MF_00163
+IPR000181 PIRSF004749
+IPR000181 PR01576
+IPR000181 PTHR10458
+IPR000181 TIGR00079
+IPR000182 PF00583
+IPR000182 PF13302
+IPR000182 PF13508
+IPR000182 PF13718
+IPR000182 PS51186
+IPR000183 PR01179
+IPR000184 PF01103
+IPR000185 MF_01382
+IPR000185 PR00906
+IPR000185 TIGR00963
+IPR000191 TIGR00577
+IPR000192 PF00266
+IPR000194 PF00006
+IPR000195 PF00566
+IPR000195 PS50086
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diff --git a/modules/t/test-genome-DBs/polyploidy/core/intron_supporting_evidence.txt b/modules/t/test-genome-DBs/polyploidy/core/intron_supporting_evidence.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/karyotype.txt b/modules/t/test-genome-DBs/polyploidy/core/karyotype.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/map.txt b/modules/t/test-genome-DBs/polyploidy/core/map.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/mapping_session.txt b/modules/t/test-genome-DBs/polyploidy/core/mapping_session.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/mapping_set.txt b/modules/t/test-genome-DBs/polyploidy/core/mapping_set.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/marker.txt b/modules/t/test-genome-DBs/polyploidy/core/marker.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/marker_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/marker_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/marker_map_location.txt b/modules/t/test-genome-DBs/polyploidy/core/marker_map_location.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/marker_synonym.txt b/modules/t/test-genome-DBs/polyploidy/core/marker_synonym.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
new file mode 100644
index 0000000000..337c9c7d21
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -0,0 +1,115 @@
+1 \N schema_type core
+2 \N schema_version 79
+3 \N patch patch_68_69_a.sql|schema_version
+4 1 species.taxonomy_id 4565
+6 1 species.alias bread wheat
+7 1 species.alias common wheat
+8 1 species.alias wheat
+9 1 species.strain Chinese Spring
+10 1 species.scientific_name Triticum aestivum
+11 1 species.production_name triticum_aestivum
+12 1 species.classification aestivum
+13 1 species.classification Triticum
+14 1 species.classification Triticeae
+15 1 species.classification Pooideae
+16 1 species.classification BEP clade
+17 1 species.classification Poaceae
+18 1 species.classification Poales
+19 1 species.classification commelinids
+20 1 species.classification Liliopsida
+21 1 species.classification Magnoliophyta
+22 1 species.classification Spermatophyta
+23 1 species.classification Euphyllophyta
+24 1 species.classification Tracheophyta
+25 1 species.classification Embryophyta
+26 1 species.classification Streptophytina
+27 1 species.classification Streptophyta
+28 1 species.classification Viridiplantae
+29 1 species.classification Eukaryota
+30 1 species.division EnsemblPlants
+31 1 assembly.name IWGSC2
+32 1 assembly.date 2014-11
+33 1 assembly.default IWGSC2
+39 1 species.display_name Triticum aestivum
+40 1 species.url Triticum_aestivum
+41 \N patch patch_69_70_a.sql|schema_version
+42 \N patch patch_69_70_b.sql|add_mapping_set_history
+43 \N patch patch_69_70_c.sql|column_datatype_consistency
+44 \N patch patch_69_70_d.sql|data_file_id_auto_increment
+45 \N patch patch_69_70_e.sql|protein_feature_hit_description
+167 1 assembly.mapping chromosome:IWGSC2#scaffold:IWGSC2
+50 1 genebuild.start_date 2014-11-IWGSC
+51 \N patch patch_70_71_a.sql|schema_version
+52 \N patch patch_70_71_b.sql|mapping_set_index
+53 \N patch patch_71_72_a.sql|schema_version
+54 \N patch patch_71_72_b.sql|associated_xref
+169 1 assembly.mapping scaffold:IWGSC2#contig
+60 \N patch patch_72_73_a.sql|schema_version
+66 1 sample.location_text 5D
+67 1 sample.location_param 5D:17389805-17402607
+69 1 repeat.analysis dust
+70 1 repeat.analysis repeatmask
+189 1 repeat_featurebuild.level toplevel
+106 1 assembly.overlapping_regions 0
+78 1 species.alias Triticum aestivum
+81 \N patch patch_72_73_b.sql|alt_allele_type
+80 1 repeat.analysis repeatmask_trep
+82 \N patch patch_72_73_c.sql|add_object_type_marker
+83 \N patch patch_73_74_a.sql|schema_version
+84 \N patch patch_73_74_b.sql|remove_dnac
+85 \N patch patch_73_74_c.sql|remove_unconventional_transcript_association
+86 \N patch patch_73_74_d.sql|remove_qtl
+87 \N patch patch_73_74_e.sql|remove_canonical_annotation
+88 \N patch patch_73_74_f.sql|remove_pair_dna_align
+89 \N patch patch_73_74_g.sql|add_transcript_idx_tise
+170 1 assembly.mapping scaffold:IWGSP1#contig
+91 \N patch patch_73_74_h.sql|alt_allele_unique_gene_idx
+187 1 genebuild.level toplevel
+94 1 genebuild.initial_release_date 2013-12-MIPS
+95 1 genebuild.last_geneset_update 2013-12-MIPS
+96 1 genebuild.version 2.2
+97 1 provider.name IWGSC
+98 1 provider.url http://www.wheatgenome.org/
+188 1 transcriptbuild.level toplevel
+100 1 genebuild.method Imported from IWGSC
+101 1 sample.transcript_param Traes_1BS_1172A6B03.1
+102 1 sample.transcript_text Traes_1BS_1172A6B03.1
+103 1 sample.gene_param Traes_1BS_1172A6B03
+104 1 sample.gene_text Traes_1BS_1172A6B03
+191 1 xref.timestamp 2014-11-25 21:31:46
+108 1 sample.search_text Calnexin
+109 \N patch patch_74_75_a.sql|schema_version
+110 \N patch patch_74_75_b.sql|transcript_source
+111 \N patch patch_74_75_c.sql|add_genome_statistics
+112 \N patch patch_74_75_d.sql|default_transcript_source
+113 \N patch patch_74_75_e.sql|unique_attrib_key
+114 \N patch patch_74_75_f.sql|longer_code
+123 1 ploidy 6
+124 \N patch patch_75_76_a.sql|schema_version
+125 \N patch patch_75_76_b.sql|allow_null_karyotype
+126 \N patch patch_75_76_c.sql|remove_alternative_splicing
+127 1 schema.load_started 2014-05-09 10:51:50
+129 1 genebuild.hash a4c20be3e15ab706859fa4ee5cc18f9d
+137 1 schema.load_complete 2014-05-09 12:30:33
+138 1 schema.load_complete 2014-05-09 12:35:10
+171 1 assembly.mapping chromosome:IWGSC2#scaffold:IWGSC2#contig
+140 1 schema.load_started 2014-05-09 15:05:28
+142 1 genebuild.hash 72373ce3078cb3394853af631d00afe2
+158 1 species.common_name bread wheat
+159 1 species.wikipedia_url http://wikipedia.org/wiki/Triticum_aestivum
+160 1 sample.variation_param BA00683163
+161 1 sample.variation_text BA00683163
+163 \N patch patch_76_77_a.sql|schema_version
+164 1 interproscan.version 5.8-49.0
+165 1 interproscan.date 20-November-2014
+166 1 interpro.version 49
+173 1 assembly.mapping scaffold:IWGSC2#scaffold:IWGSP1
+174 1 liftover.mapping scaffold:IWGSC2#scaffold:IWGSP1
+175 1 assembly.mapping chromosome:IWGSC2#scaffold:IWGSP1
+190 1 liftover.mapping chromosome:IWGSC2#scaffold:IWGSP1
+178 1 repeat.analysis ena_repeat
+179 1 repeat.analysis ena_repeat_direct
+192 \N patch patch_77_78_a.sql|schema_version
+193 \N patch patch_77_78_b.sql|source_column_increase
+194 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+195 \N patch patch_78_79_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta_coord.txt b/modules/t/test-genome-DBs/polyploidy/core/meta_coord.txt
new file mode 100644
index 0000000000..c170da6da4
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta_coord.txt
@@ -0,0 +1,4 @@
+gene 8 35335
+transcript 8 35059
+repeat_feature 8 18170
+exon 8 7827
diff --git a/modules/t/test-genome-DBs/polyploidy/core/misc_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/misc_attrib.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/misc_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/misc_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/misc_feature_misc_set.txt b/modules/t/test-genome-DBs/polyploidy/core/misc_feature_misc_set.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/misc_set.txt b/modules/t/test-genome-DBs/polyploidy/core/misc_set.txt
new file mode 100644
index 0000000000..14e251783d
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/misc_set.txt
@@ -0,0 +1,18 @@
+1 encode Encode regions Regions that were examined in the <a rel="external" href="http://www.genome.gov/10005107">Encode</a> pilot project. 1877426
+2 genomicctg Genomic contigs The largest contigs constructed by the Genome Reference Consortium, <a rel="external" href="http://genomereference.org">GRC</a>, for this genomic assembly. 100530253
+3 tilepath Tilepath BAC clones upon which the current genomic assembly was based. Colours indicate a finished sequence (gold clones), phase 1 sequencing (dark pink), phase 0 (light pink) or other (grey). Clones that have been fluorescence in situ hybridisation (FISH) mapped are marked with a black triangle in the top left corner. If a clone is shown in outline, the mapping to the genome is problematic and the true length may not be displayed. 1071649
+9 encode_excluded ENCODE excluded regions Genomic regions that have been identified as problematic in the human genome by the ENCODE project. These regions contain abnormally high unique-mapping read coverage signal in open chromatin and control/input datasets across many cell lines and are classified as dispersed high mappability artifacts, dispersed low mappability artifacts, satellite repeats, centromeric repeats, telomeric repeats or snRNA repeats. 4132352
+10 bac_map BAC map Full list of mapped BAC clones 500000
+11 ASSEMBLY WGS/Clones assembly The tiling path of clones and WGS contigs 1000000
+12 bacs BACs BACs 13738670
+13 gap gaps 44494
+14 matepairs Mate pairs Inconsistent mate pairs 21557510
+15 atag_CLE Assembly tag Clone_left_end 1000000
+16 atag_CRE Assembly tag Clone_right_end 1000000
+17 atag_Misc Assembly tag Misc 1000000
+18 atag_Unsure Assembly tag Unsure 1000000
+19 CHORI-17 CHORI-17 library Mapped clone end sequences from human CHORI-17 BAC library (CH17) 18090412
+20 RPCI-11 RPCI-11 library Mapped clone end sequences from human RPCI-11 BAC library (RP11) 18084827
+21 ABC ABC libraries Mapped clone end sequences from ABCs (ABC7, ABC8, ABC9, ABC10, ABC11, ABC12, ABC13, ABC14, ABC16, ABC21, ABC22, ABC24, ABC27) human fosmid libraries (ABC) 18047227
+22 WIBR-2 WIBR-2 library Mapped clone end sequences from WIBR-2 human fosmid library (WI2) 18043599
+23 CH243 CHORI-243 library Mapped clone end sequences from sheep CHORI-243 BAC library (CH243) 197393133
diff --git a/modules/t/test-genome-DBs/polyploidy/core/object_xref.txt b/modules/t/test-genome-DBs/polyploidy/core/object_xref.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/ontology_xref.txt b/modules/t/test-genome-DBs/polyploidy/core/ontology_xref.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/operon.txt b/modules/t/test-genome-DBs/polyploidy/core/operon.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/operon_transcript.txt b/modules/t/test-genome-DBs/polyploidy/core/operon_transcript.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/operon_transcript_gene.txt b/modules/t/test-genome-DBs/polyploidy/core/operon_transcript_gene.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/peptide_archive.txt b/modules/t/test-genome-DBs/polyploidy/core/peptide_archive.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/prediction_exon.txt b/modules/t/test-genome-DBs/polyploidy/core/prediction_exon.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/prediction_transcript.txt b/modules/t/test-genome-DBs/polyploidy/core/prediction_transcript.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/protein_align_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/protein_align_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/protein_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/protein_feature.txt
new file mode 100644
index 0000000000..9ac605eba6
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/protein_feature.txt
@@ -0,0 +1,47 @@
+3177572 79459 29 51 0 0 TMhelix 197 \N \N \N \N \N
+3177573 79459 2 24 0 0 TMhelix 197 \N \N \N \N \N
+3311591 116850 174 188 0 0 PR00320 190 \N 0.0000019 \N \N G-protein beta WD-40 repeat
+3311578 116850 95 109 0 0 PR00320 190 \N 0.0000019 \N \N G-protein beta WD-40 repeat
+3311567 116850 134 148 0 0 PR00320 190 \N 0.0000019 \N \N G-protein beta WD-40 repeat
+3311551 116850 11 236 0 0 SSF50978 193 \N 0 \N \N WD40-repeat-containing domain
+3311537 116850 31 69 1 46 SM00320 192 166.8 0 \N \N WD40 repeat
+3311527 116850 70 108 1 46 SM00320 192 166.8 0 \N \N WD40 repeat
+3311515 116850 149 187 1 46 SM00320 192 166.8 0 \N \N WD40 repeat
+3311501 116850 109 147 1 46 SM00320 192 166.8 0 \N \N WD40 repeat
+3311490 116850 188 225 1 46 SM00320 192 166.8 0 \N \N WD40 repeat
+3311475 116850 73 108 3 39 PF00400 187 128.8 0 \N \N WD40 repeat
+3311465 116850 195 224 8 38 PF00400 187 128.8 0 \N \N WD40 repeat
+3311454 116850 32 68 1 38 PF00400 187 128.8 0 \N \N WD40 repeat
+3311442 116850 112 146 3 38 PF00400 187 128.8 0 \N \N WD40 repeat
+3311427 116850 150 187 1 39 PF00400 187 128.8 0 \N \N WD40 repeat
+3311416 116850 13 234 65 318 2.130.10.10 184 160.8 0 \N \N WD40/YVTN repeat-like-containing domain
+3311403 116850 15 29 0 0 PS00678 191 \N \N \N \N WD40 repeat, conserved site
+3311402 116850 2 244 0 0 PTHR19849:SF0 186 0 0 \N \N \N
+3311401 116850 2 244 0 0 PTHR19849 186 0 0 \N \N \N
+3311393 116850 1 187 0 0 PS50294 188 \N \N \N \N WD40-repeat-containing domain
+3311379 116850 38 68 0 0 PS50082 188 \N \N \N \N WD40 repeat
+3311366 116850 156 187 0 0 PS50082 188 \N \N \N \N WD40 repeat
+3311358 116850 116 156 0 0 PS50082 188 \N \N \N \N WD40 repeat
+3311347 116850 77 108 0 0 PS50082 188 \N \N \N \N WD40 repeat
+2810996 79459 4 16 0 0 seg 198 \N \N \N \N \N
+2812327 79141 77 88 0 0 seg 198 \N \N \N \N \N
+2812328 79141 98 115 0 0 seg 198 \N \N \N \N \N
+3342879 124987 1 81 0 0 PTHR31973 186 0 0 \N \N \N
+3382702 123920 1 68 0 0 PTHR31973 186 0 0 \N \N \N
+3382703 123920 1 67 26 88 PF10551 187 65.3 0 \N \N MULE transposase domain
+3451494 80726 1 66 0 0 MF_00531 185 \N \N \N \N Ribosomal protein S19/S15
+3451508 80726 2 67 0 0 PTHR11880:SF8 186 0 0 \N \N \N
+3451509 80726 2 67 0 0 PTHR11880 186 0 0 \N \N Ribosomal protein S19/S15
+3451523 80726 30 54 0 0 PS00323 191 \N \N \N \N Ribosomal protein S19 conserved site
+3451533 80726 2 59 23 80 PF00203 187 99.1 0 \N \N Ribosomal protein S19/S15
+3451549 80726 2 67 25 90 3a1pB00 184 95.5 0 \N \N Ribosomal protein S19, superfamily
+3451563 80726 2 68 25 91 TIGR01050 194 96.9 0 \N \N Ribosomal protein S19, bacterial-type
+3451585 80726 1 70 1 149 PIRSF002144 189 47.7 0 \N \N Ribosomal protein S19/S15
+3451600 80726 2 61 0 0 SSF54570 193 \N 0 \N \N Ribosomal protein S19, superfamily
+3451613 80726 30 42 0 0 PR00975 190 \N 4.1e-23 \N \N Ribosomal protein S19/S15
+3451631 80726 10 29 0 0 PR00975 190 \N 4.1e-23 \N \N Ribosomal protein S19/S15
+3451641 80726 42 57 0 0 PR00975 190 \N 4.1e-23 \N \N Ribosomal protein S19/S15
+3502912 79459 10 54 0 0 MF_00441 185 \N \N \N \N Photosystem II PsbK
+3502922 79459 14 54 2 42 PF02533 187 79.5 0 \N \N Photosystem II PsbK
+3502931 79459 18 54 0 0 0053716 193 \N 0 \N \N \N
+3502932 79459 18 54 0 0 PD004458 183 \N \N \N \N Photosystem II PsbK
diff --git a/modules/t/test-genome-DBs/polyploidy/core/repeat_consensus.txt b/modules/t/test-genome-DBs/polyploidy/core/repeat_consensus.txt
new file mode 100644
index 0000000000..fbd86d5376
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/repeat_consensus.txt
@@ -0,0 +1,17 @@
+1163918 trf trf Tandem repeats CTGCAATATTCACTTGCTCTC
+1163915 trf trf Tandem repeats ACTTGTTCTGCTCTTGT
+1163913 trf trf Tandem repeats TAGTAAAATTCAAAAGAAAA
+1163911 trf trf Tandem repeats ATTCACTTGCTCTGCTCTTGTACTGAACTGAAC
+1163907 trf trf Tandem repeats ACCAAAAGGACATAGTTCAGTACATGATA
+1163894 trf trf Tandem repeats AATCCTCATCAGAAGAAT
+1022815 trf trf Tandem repeats TGTACTTATGAAATCACAATC
+1022812 trf trf Tandem repeats ATAGTATAAGAAAAACAA
+1022810 trf trf Tandem repeats TTTATTTCATTTCTATAGTATAAGAAAAACAA
+1022807 trf trf Tandem repeats TACTTGTCTTTCTAGGCATTTCAAATGACTATCACATACGGATGTATGTAGACATATTTTAGAGTGTAGATTCACTCATTTTACTCCGTATGTAGTCACTTGTTGAAATGCCTAGAAAGACAAGTATTTAGGAACGGAGGGAG
+942309 dust dust Dust N
+941541 HADES_TA DNA/TcMar-Stowaway Type II Transposons N
+941900 gnl|TREP|TREP3092 Unknown Unknown N
+941902 gnl|TREP|TREP3081 Unknown Unknown N
+941943 gnl|TREP|TREP3528 Unknown Unknown N
+941955 gnl|TREP|TREP3107 Unknown Unknown N
+941971 gnl|TREP|TREP3051 Unknown Unknown N
diff --git a/modules/t/test-genome-DBs/polyploidy/core/repeat_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/repeat_feature.txt
new file mode 100644
index 0000000000..f1f2a2b2f3
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/repeat_feature.txt
@@ -0,0 +1,68 @@
+5625321 3495727 14718 14833 1 3 112 941900 181 355
+5625322 3495727 16725 16888 -1 1 162 941955 181 1003
+5625323 3495727 16892 17031 -1 1 138 941955 181 881
+5625325 3495727 17035 17174 -1 1 138 941955 181 839
+5625327 3495727 18070 18301 -1 1677 1908 941971 181 779
+8662306 3495794 255 381 -1 1 112 941900 181 670
+8662307 3495794 3690 3774 -1 1 85 941902 181 564
+8662308 3495794 4198 4266 -1 1 71 941943 181 302
+5329914 3495794 4217 4266 1 47 97 941541 180 329
+10446797 3495794 4161 4168 0 4161 4168 942309 177 0
+10446792 3495794 2866 2872 0 2866 2872 942309 177 0
+10446784 3495794 2386 2394 0 2386 2394 942309 177 0
+10446778 3495794 2176 2205 0 2176 2205 942309 177 0
+10446771 3495794 1184 1191 0 1184 1191 942309 177 0
+10446766 3495794 1138 1144 0 1138 1144 942309 177 0
+9925409 3495644 1615 1621 0 1615 1621 942309 177 0
+9925406 3495644 1486 1492 0 1486 1492 942309 177 0
+9451525 3495727 17477 17559 0 17477 17559 942309 177 0
+9451522 3495727 15974 15980 0 15974 15980 942309 177 0
+9451520 3495727 12328 12334 0 12328 12334 942309 177 0
+9451518 3495727 10480 10486 0 10480 10486 942309 177 0
+9451515 3495727 10317 10323 0 10317 10323 942309 177 0
+9451510 3495727 10169 10176 0 10169 10176 942309 177 0
+9451507 3495727 10000 10006 0 10000 10006 942309 177 0
+9451504 3495727 9866 9872 0 9866 9872 942309 177 0
+9451501 3495727 9664 9670 0 9664 9670 942309 177 0
+9451498 3495727 9536 9543 0 9536 9543 942309 177 0
+9451495 3495727 9393 9400 0 9393 9400 942309 177 0
+9451492 3495727 9336 9343 0 9336 9343 942309 177 0
+9451489 3495727 9301 9329 0 9301 9329 942309 177 0
+9451486 3495727 9061 9075 0 9061 9075 942309 177 0
+9451483 3495727 8888 8894 0 8888 8894 942309 177 0
+9451479 3495727 8772 8778 0 8772 8778 942309 177 0
+9451477 3495727 8612 8618 0 8612 8618 942309 177 0
+9451473 3495727 8196 8202 0 8196 8202 942309 177 0
+9451469 3495727 7753 7759 0 7753 7759 942309 177 0
+9451464 3495727 7463 7469 0 7463 7469 942309 177 0
+9451460 3495727 7241 7247 0 7241 7247 942309 177 0
+9451455 3495727 6867 6876 0 6867 6876 942309 177 0
+9451452 3495727 6284 6300 0 6284 6300 942309 177 0
+9451446 3495727 6220 6226 0 6220 6226 942309 177 0
+9451442 3495727 6145 6152 0 6145 6152 942309 177 0
+9451438 3495727 6050 6056 0 6050 6056 942309 177 0
+9451431 3495727 5665 5678 0 5665 5678 942309 177 0
+9451424 3495727 5533 5544 0 5533 5544 942309 177 0
+9451417 3495727 5513 5520 0 5513 5520 942309 177 0
+9451408 3495727 4719 4725 0 4719 4725 942309 177 0
+9451405 3495727 4650 4657 0 4650 4657 942309 177 0
+9451403 3495727 4440 4448 0 4440 4448 942309 177 0
+9451401 3495727 3869 3944 0 3869 3944 942309 177 0
+9451399 3495727 3666 3672 0 3666 3672 942309 177 0
+9451397 3495727 1796 1802 0 1796 1802 942309 177 0
+9451395 3495727 1760 1774 0 1760 1774 942309 177 0
+9451393 3495727 1672 1686 0 1672 1686 942309 177 0
+9451390 3495727 1423 1431 0 1423 1431 942309 177 0
+9451387 3495727 1299 1305 0 1299 1305 942309 177 0
+9451384 3495727 1047 1053 0 1047 1053 942309 177 0
+9451379 3495727 757 867 0 757 867 942309 177 0
+9399608 3495644 3610 3717 0 1 108 1163918 178 174
+9399600 3495644 3705 3758 0 1 54 1163915 178 57
+9399592 3495644 1400 1451 0 1 52 1163913 178 76
+9399581 3495644 3701 3766 0 1 66 1163911 178 90
+9399564 3495644 1030 1114 0 1 85 1163907 178 121
+9399530 3495644 3349 3384 0 1 36 1163894 178 51
+9072905 3495727 13368 13432 0 1 65 1022815 178 116
+9072902 3495727 10505 10542 0 1 38 1022812 178 76
+9072898 3495727 10460 10522 0 1 63 1022810 178 103
+9072892 3495727 16744 17174 0 1 431 1022807 178 820
diff --git a/modules/t/test-genome-DBs/polyploidy/core/seq_region.txt b/modules/t/test-genome-DBs/polyploidy/core/seq_region.txt
new file mode 100644
index 0000000000..f24fb23081
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/seq_region.txt
@@ -0,0 +1,6 @@
+3116582 IWGSC_CSS_5AL_contig_316991 7 5428
+3309354 IWGSC_CSS_6BS_contig_3758 7 4562
+3355688 IWGSC_CSS_6DS_contig_94739 7 18301
+3495644 IWGSC_CSS_6BS_scaff_233977 8 4562
+3495727 IWGSC_CSS_6DS_scaff_2121653 8 18301
+3495794 IWGSC_CSS_5AL_scaff_2697823 8 5428
diff --git a/modules/t/test-genome-DBs/polyploidy/core/seq_region_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/seq_region_attrib.txt
new file mode 100644
index 0000000000..9586de5c41
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/seq_region_attrib.txt
@@ -0,0 +1,9 @@
+3495794 425 A
+3495644 425 B
+3495794 6 1
+3495727 6 1
+3495644 6 1
+3495644 64 2
+3495727 64 3
+3495794 64 1
+3495727 425 D
diff --git a/modules/t/test-genome-DBs/polyploidy/core/seq_region_mapping.txt b/modules/t/test-genome-DBs/polyploidy/core/seq_region_mapping.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/seq_region_synonym.txt b/modules/t/test-genome-DBs/polyploidy/core/seq_region_synonym.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/simple_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/simple_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/stable_id_event.txt b/modules/t/test-genome-DBs/polyploidy/core/stable_id_event.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/supporting_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/supporting_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
new file mode 100644
index 0000000000..39e3669dcb
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -0,0 +1,887 @@
+CREATE TABLE `alt_allele` (
+ `alt_allele_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `alt_allele_group_id` int(10) unsigned NOT NULL,
+ `gene_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`alt_allele_id`),
+ UNIQUE KEY `gene_idx` (`gene_id`),
+ KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `alt_allele_attrib` (
+ `alt_allele_id` int(10) unsigned DEFAULT NULL,
+ `attrib` enum('IS_REPRESENTATIVE','IS_MOST_COMMON_ALLELE','IN_CORRECTED_ASSEMBLY','HAS_CODING_POTENTIAL','IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY','IN_SYNTENIC_REGION','HAS_SAME_UNDERLYING_DNA_SEQUENCE','IN_BROKEN_ASSEMBLY_REGION','IS_VALID_ALTERNATE','SAME_AS_REPRESENTATIVE','SAME_AS_ANOTHER_ALLELE','MANUALLY_ASSIGNED','AUTOMATICALLY_ASSIGNED') DEFAULT NULL,
+ KEY `aa_idx` (`alt_allele_id`,`attrib`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `alt_allele_group` (
+ `alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ PRIMARY KEY (`alt_allele_group_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `analysis` (
+ `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `logic_name` varchar(128) NOT NULL,
+ `db` varchar(120) DEFAULT NULL,
+ `db_version` varchar(40) DEFAULT NULL,
+ `db_file` varchar(120) DEFAULT NULL,
+ `program` varchar(80) DEFAULT NULL,
+ `program_version` varchar(40) DEFAULT NULL,
+ `program_file` varchar(80) DEFAULT NULL,
+ `parameters` text,
+ `module` varchar(80) DEFAULT NULL,
+ `module_version` varchar(40) DEFAULT NULL,
+ `gff_source` varchar(40) DEFAULT NULL,
+ `gff_feature` varchar(40) DEFAULT NULL,
+ PRIMARY KEY (`analysis_id`),
+ UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `analysis_description` (
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `description` text,
+ `display_label` varchar(255) NOT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text,
+ UNIQUE KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `assembly` (
+ `asm_seq_region_id` int(10) unsigned NOT NULL,
+ `cmp_seq_region_id` int(10) unsigned NOT NULL,
+ `asm_start` int(10) NOT NULL,
+ `asm_end` int(10) NOT NULL,
+ `cmp_start` int(10) NOT NULL,
+ `cmp_end` int(10) NOT NULL,
+ `ori` tinyint(4) NOT NULL,
+ UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
+ KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `assembly_exception` (
+ `assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
+ `exc_seq_region_id` int(10) unsigned NOT NULL,
+ `exc_seq_region_start` int(10) unsigned NOT NULL,
+ `exc_seq_region_end` int(10) unsigned NOT NULL,
+ `ori` int(11) NOT NULL,
+ PRIMARY KEY (`assembly_exception_id`),
+ KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `associated_group` (
+ `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `description` varchar(128) DEFAULT NULL,
+ PRIMARY KEY (`associated_group_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `associated_xref` (
+ `associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ `condition_type` varchar(128) DEFAULT NULL,
+ `associated_group_id` int(10) unsigned DEFAULT NULL,
+ `rank` int(10) unsigned DEFAULT '0',
+ PRIMARY KEY (`associated_xref_id`),
+ UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
+ KEY `associated_source_idx` (`source_xref_id`),
+ KEY `associated_object_idx` (`object_xref_id`),
+ KEY `associated_idx` (`xref_id`),
+ KEY `associated_group_idx` (`associated_group_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `attrib_type` (
+ `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(20) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text,
+ PRIMARY KEY (`attrib_type_id`),
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `coord_system` (
+ `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
+ `name` varchar(40) NOT NULL,
+ `version` varchar(255) DEFAULT NULL,
+ `rank` int(11) NOT NULL,
+ `attrib` set('default_version','sequence_level') DEFAULT NULL,
+ PRIMARY KEY (`coord_system_id`),
+ UNIQUE KEY `rank_idx` (`rank`,`species_id`),
+ UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
+ KEY `species_idx` (`species_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `data_file` (
+ `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `name` varchar(100) NOT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
+ `file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
+ PRIMARY KEY (`data_file_id`),
+ UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
+ KEY `df_name_idx` (`name`),
+ KEY `df_analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `density_feature` (
+ `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `density_value` float NOT NULL,
+ PRIMARY KEY (`density_feature_id`),
+ KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
+ KEY `seq_region_id_idx` (`seq_region_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `density_type` (
+ `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `block_size` int(11) NOT NULL,
+ `region_features` int(11) NOT NULL,
+ `value_type` enum('sum','ratio') NOT NULL,
+ PRIMARY KEY (`density_type_id`),
+ UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `dependent_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL,
+ `master_xref_id` int(10) unsigned NOT NULL,
+ `dependent_xref_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`object_xref_id`),
+ KEY `dependent` (`dependent_xref_id`),
+ KEY `master_idx` (`master_xref_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `ditag` (
+ `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) NOT NULL,
+ `type` varchar(30) NOT NULL,
+ `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
+ `sequence` tinytext NOT NULL,
+ PRIMARY KEY (`ditag_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `ditag_feature` (
+ `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` tinytext NOT NULL,
+ `ditag_side` enum('F','L','R') NOT NULL,
+ PRIMARY KEY (`ditag_feature_id`),
+ KEY `ditag_idx` (`ditag_id`),
+ KEY `ditag_pair_idx` (`ditag_pair_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `dna` (
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `sequence` longtext NOT NULL,
+ PRIMARY KEY (`seq_region_id`)
+) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000 CHECKSUM=1;
+
+CREATE TABLE `dna_align_feature` (
+ `dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(1) NOT NULL,
+ `hit_start` int(11) NOT NULL,
+ `hit_end` int(11) NOT NULL,
+ `hit_strand` tinyint(1) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `cigar_line` text,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
+ `hcoverage` double DEFAULT NULL,
+ `external_data` text,
+ PRIMARY KEY (`dna_align_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
+ KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
+ KEY `hit_idx` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`)
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
+
+CREATE TABLE `exon` (
+ `exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `phase` tinyint(2) NOT NULL,
+ `end_phase` tinyint(2) NOT NULL,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`exon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `exon_transcript` (
+ `exon_id` int(10) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `rank` int(10) NOT NULL,
+ PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
+ KEY `transcript` (`transcript_id`),
+ KEY `exon` (`exon_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `external_db` (
+ `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `db_name` varchar(100) NOT NULL,
+ `db_release` varchar(255) DEFAULT NULL,
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
+ `priority` int(11) NOT NULL,
+ `db_display_name` varchar(255) DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
+ `secondary_db_name` varchar(255) DEFAULT NULL,
+ `secondary_db_table` varchar(255) DEFAULT NULL,
+ `description` text,
+ PRIMARY KEY (`external_db_id`),
+ UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `external_synonym` (
+ `xref_id` int(10) unsigned NOT NULL,
+ `synonym` varchar(100) NOT NULL,
+ PRIMARY KEY (`xref_id`,`synonym`),
+ KEY `name_index` (`synonym`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `gene` (
+ `gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `biotype` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_xref_id` int(10) unsigned DEFAULT NULL,
+ `source` varchar(40) NOT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `canonical_transcript_id` int(10) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`gene_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `xref_id_index` (`display_xref_id`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`),
+ KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `gene_archive` (
+ `gene_stable_id` varchar(128) NOT NULL,
+ `gene_version` smallint(6) NOT NULL DEFAULT '1',
+ `transcript_stable_id` varchar(128) NOT NULL,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '1',
+ `translation_stable_id` varchar(128) DEFAULT NULL,
+ `translation_version` smallint(6) NOT NULL DEFAULT '1',
+ `peptide_archive_id` int(10) unsigned DEFAULT NULL,
+ `mapping_session_id` int(10) unsigned NOT NULL,
+ KEY `gene_idx` (`gene_stable_id`,`gene_version`),
+ KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+ KEY `peptide_archive_id_idx` (`peptide_archive_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `gene_attrib` (
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `genome_statistics` (
+ `genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `statistic` varchar(128) NOT NULL,
+ `value` int(10) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
+ `attrib_type_id` int(10) unsigned DEFAULT NULL,
+ `timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`genome_statistics_id`),
+ UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
+ KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `identity_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL,
+ `xref_identity` int(5) DEFAULT NULL,
+ `ensembl_identity` int(5) DEFAULT NULL,
+ `xref_start` int(11) DEFAULT NULL,
+ `xref_end` int(11) DEFAULT NULL,
+ `ensembl_start` int(11) DEFAULT NULL,
+ `ensembl_end` int(11) DEFAULT NULL,
+ `cigar_line` text,
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ PRIMARY KEY (`object_xref_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `interpro` (
+ `interpro_ac` varchar(40) NOT NULL,
+ `id` varchar(40) NOT NULL,
+ UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+ KEY `id_idx` (`id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `intron_supporting_evidence` (
+ `intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `hit_name` varchar(100) NOT NULL,
+ `score` decimal(10,3) DEFAULT NULL,
+ `score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`intron_supporting_evidence_id`),
+ UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `karyotype` (
+ `karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `band` varchar(40) DEFAULT NULL,
+ `stain` varchar(40) DEFAULT NULL,
+ PRIMARY KEY (`karyotype_id`),
+ KEY `region_band_idx` (`seq_region_id`,`band`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `map` (
+ `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `map_name` varchar(30) NOT NULL,
+ PRIMARY KEY (`map_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `mapping_session` (
+ `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `old_db_name` varchar(80) NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) NOT NULL DEFAULT '',
+ `old_release` varchar(5) NOT NULL DEFAULT '',
+ `new_release` varchar(5) NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) NOT NULL DEFAULT '',
+ `created` datetime NOT NULL,
+ PRIMARY KEY (`mapping_session_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `mapping_set` (
+ `mapping_set_id` int(10) unsigned NOT NULL,
+ `internal_schema_build` varchar(20) NOT NULL,
+ `external_schema_build` varchar(20) NOT NULL,
+ PRIMARY KEY (`mapping_set_id`),
+ UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `marker` (
+ `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
+ `left_primer` varchar(100) NOT NULL,
+ `right_primer` varchar(100) NOT NULL,
+ `min_primer_dist` int(10) unsigned NOT NULL,
+ `max_primer_dist` int(10) unsigned NOT NULL,
+ `priority` int(11) DEFAULT NULL,
+ `type` enum('est','microsatellite') DEFAULT NULL,
+ PRIMARY KEY (`marker_id`),
+ KEY `marker_idx` (`marker_id`,`priority`),
+ KEY `display_idx` (`display_marker_synonym_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `marker_feature` (
+ `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `marker_id` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `map_weight` int(10) unsigned DEFAULT NULL,
+ PRIMARY KEY (`marker_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `marker_map_location` (
+ `marker_id` int(10) unsigned NOT NULL,
+ `map_id` int(10) unsigned NOT NULL,
+ `chromosome_name` varchar(15) NOT NULL,
+ `marker_synonym_id` int(10) unsigned NOT NULL,
+ `position` varchar(15) NOT NULL,
+ `lod_score` double DEFAULT NULL,
+ PRIMARY KEY (`marker_id`,`map_id`),
+ KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `marker_synonym` (
+ `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `marker_id` int(10) unsigned NOT NULL,
+ `source` varchar(20) DEFAULT NULL,
+ `name` varchar(50) DEFAULT NULL,
+ PRIMARY KEY (`marker_synonym_id`),
+ KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
+ KEY `marker_idx` (`marker_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `meta` (
+ `meta_id` int(11) NOT NULL AUTO_INCREMENT,
+ `species_id` int(10) unsigned DEFAULT '1',
+ `meta_key` varchar(40) NOT NULL,
+ `meta_value` varchar(255) DEFAULT NULL,
+ PRIMARY KEY (`meta_id`),
+ UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
+ KEY `species_value_idx` (`species_id`,`meta_value`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `meta_coord` (
+ `table_name` varchar(40) NOT NULL,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `max_length` int(11) DEFAULT NULL,
+ UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `misc_attrib` (
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `misc_feature` (
+ `misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `misc_feature_misc_set` (
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
+ KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `misc_set` (
+ `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(25) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text NOT NULL,
+ `max_length` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`misc_set_id`),
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `object_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL,
+ `linkage_annotation` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`object_xref_id`),
+ UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+ KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `ontology_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ `linkage_type` varchar(3) DEFAULT NULL,
+ UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `source_idx` (`source_xref_id`),
+ KEY `object_idx` (`object_xref_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `operon` (
+ `operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`operon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `name_idx` (`display_label`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `operon_transcript` (
+ `operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `operon_id` int(10) unsigned NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`operon_transcript_id`),
+ KEY `operon_idx` (`operon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `operon_transcript_gene` (
+ `operon_transcript_id` int(10) unsigned DEFAULT NULL,
+ `gene_id` int(10) unsigned DEFAULT NULL,
+ KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `peptide_archive` (
+ `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `md5_checksum` varchar(32) DEFAULT NULL,
+ `peptide_seq` mediumtext NOT NULL,
+ PRIMARY KEY (`peptide_archive_id`),
+ KEY `checksum` (`md5_checksum`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `prediction_exon` (
+ `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `prediction_transcript_id` int(10) unsigned NOT NULL,
+ `exon_rank` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(4) NOT NULL,
+ `start_phase` tinyint(4) NOT NULL,
+ `score` double DEFAULT NULL,
+ `p_value` double DEFAULT NULL,
+ PRIMARY KEY (`prediction_exon_id`),
+ KEY `transcript_idx` (`prediction_transcript_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `prediction_transcript` (
+ `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(4) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
+ PRIMARY KEY (`prediction_transcript_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `protein_align_feature` (
+ `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL,
+ `hit_end` int(10) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `cigar_line` text,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
+ `hcoverage` double DEFAULT NULL,
+ PRIMARY KEY (`protein_align_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
+ KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
+ KEY `hit_idx` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`)
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
+
+CREATE TABLE `protein_feature` (
+ `protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `translation_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `seq_end` int(10) NOT NULL,
+ `hit_start` int(10) NOT NULL,
+ `hit_end` int(10) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `external_data` text,
+ `hit_description` text,
+ PRIMARY KEY (`protein_feature_id`),
+ KEY `translation_idx` (`translation_id`),
+ KEY `hitname_idx` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `repeat_consensus` (
+ `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `repeat_name` varchar(255) NOT NULL,
+ `repeat_class` varchar(100) NOT NULL,
+ `repeat_type` varchar(40) NOT NULL,
+ `repeat_consensus` text,
+ PRIMARY KEY (`repeat_consensus_id`),
+ KEY `name` (`repeat_name`),
+ KEY `class` (`repeat_class`),
+ KEY `consensus` (`repeat_consensus`(10)),
+ KEY `type` (`repeat_type`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `repeat_feature` (
+ `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL,
+ `repeat_end` int(10) NOT NULL,
+ `repeat_consensus_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double DEFAULT NULL,
+ PRIMARY KEY (`repeat_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `repeat_idx` (`repeat_consensus_id`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
+
+CREATE TABLE `seq_region` (
+ `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(40) NOT NULL,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `length` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`seq_region_id`),
+ UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+ KEY `cs_idx` (`coord_system_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `seq_region_attrib` (
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `seq_region_mapping` (
+ `external_seq_region_id` int(10) unsigned NOT NULL,
+ `internal_seq_region_id` int(10) unsigned NOT NULL,
+ `mapping_set_id` int(10) unsigned NOT NULL,
+ KEY `mapping_set_idx` (`mapping_set_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `seq_region_synonym` (
+ `seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `synonym` varchar(40) NOT NULL,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
+ PRIMARY KEY (`seq_region_synonym_id`),
+ UNIQUE KEY `syn_idx` (`synonym`),
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `simple_feature` (
+ `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(1) NOT NULL,
+ `display_label` varchar(255) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double DEFAULT NULL,
+ PRIMARY KEY (`simple_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `hit_idx` (`display_label`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `stable_id_event` (
+ `old_stable_id` varchar(128) DEFAULT NULL,
+ `old_version` smallint(6) DEFAULT NULL,
+ `new_stable_id` varchar(128) DEFAULT NULL,
+ `new_version` smallint(6) DEFAULT NULL,
+ `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL,
+ `score` float NOT NULL DEFAULT '0',
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ KEY `new_idx` (`new_stable_id`),
+ KEY `old_idx` (`old_stable_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `supporting_feature` (
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+ `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
+ KEY `feature_idx` (`feature_type`,`feature_id`)
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
+
+CREATE TABLE `transcript` (
+ `transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `gene_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_xref_id` int(10) unsigned DEFAULT NULL,
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
+ `biotype` varchar(40) NOT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `canonical_translation_id` int(10) unsigned DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`transcript_id`),
+ UNIQUE KEY `canonical_translation_idx` (`canonical_translation_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `gene_index` (`gene_id`),
+ KEY `xref_id_index` (`display_xref_id`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `transcript_attrib` (
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `transcript_intron_supporting_evidence` (
+ `transcript_id` int(10) unsigned NOT NULL,
+ `intron_supporting_evidence_id` int(10) unsigned NOT NULL,
+ `previous_exon_id` int(10) unsigned NOT NULL,
+ `next_exon_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`),
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `transcript_supporting_feature` (
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+ `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
+ KEY `feature_idx` (`feature_type`,`feature_id`)
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
+
+CREATE TABLE `translation` (
+ `translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `start_exon_id` int(10) unsigned NOT NULL,
+ `seq_end` int(10) NOT NULL,
+ `end_exon_id` int(10) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`translation_id`),
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `translation_attrib` (
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `unmapped_object` (
+ `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `type` enum('xref','cDNA','Marker') NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
+ `identifier` varchar(255) NOT NULL,
+ `unmapped_reason_id` int(10) unsigned NOT NULL,
+ `query_score` double DEFAULT NULL,
+ `target_score` double DEFAULT NULL,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
+ `parent` varchar(255) DEFAULT NULL,
+ PRIMARY KEY (`unmapped_object_id`),
+ UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
+ KEY `id_idx` (`identifier`(50)),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
+ KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `unmapped_reason` (
+ `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `summary_description` varchar(255) DEFAULT NULL,
+ `full_description` varchar(255) DEFAULT NULL,
+ PRIMARY KEY (`unmapped_reason_id`)
+) ENGINE=MyISAM CHECKSUM=1;
+
+CREATE TABLE `xref` (
+ `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `external_db_id` int(10) unsigned NOT NULL,
+ `dbprimary_acc` varchar(128) DEFAULT NULL,
+ `display_label` varchar(128) NOT NULL,
+ `version` varchar(10) NOT NULL DEFAULT '0',
+ `description` text,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) NOT NULL DEFAULT '',
+ PRIMARY KEY (`xref_id`),
+ UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
+ KEY `display_index` (`display_label`),
+ KEY `info_type_idx` (`info_type`)
+) ENGINE=MyISAM CHECKSUM=1;
+
diff --git a/modules/t/test-genome-DBs/polyploidy/core/transcript.txt b/modules/t/test-genome-DBs/polyploidy/core/transcript.txt
new file mode 100644
index 0000000000..8252d09352
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/transcript.txt
@@ -0,0 +1,6 @@
+79141 23688 119 3495727 898 1416 -1 \N ensembl protein_coding NOVEL \N 1 79141 Traes_6DS_3B68FB2E11.1 1 2014-01-21 14:05:47 2014-01-21 14:05:47
+79459 23830 119 3495727 8829 9015 1 \N ensembl protein_coding NOVEL \N 1 79459 Traes_6DS_F1A510F0D1.1 1 2014-01-21 14:05:48 2014-01-21 14:05:48
+80726 24399 119 3495727 1853 2068 1 665630 ensembl protein_coding KNOWN \N 1 80726 Traes_6DS_262C704652.1 1 2014-01-21 14:05:56 2014-01-21 14:05:56
+116850 37263 119 3495794 506 4791 -1 \N ensembl protein_coding NOVEL \N 1 116850 Traes_5AL_7256A9F19.3 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+123920 39717 119 3495644 2408 2611 -1 \N ensembl protein_coding NOVEL \N 1 123920 Traes_6BS_5FDE5650B.1 1 2014-01-21 14:18:24 2014-01-21 14:18:24
+124987 40233 119 3495644 2030 2272 -1 \N ensembl protein_coding NOVEL \N 1 124987 Traes_6BS_48A5D59CE.1 1 2014-01-21 14:18:30 2014-01-21 14:18:30
diff --git a/modules/t/test-genome-DBs/polyploidy/core/transcript_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/transcript_attrib.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/transcript_intron_supporting_evidence.txt b/modules/t/test-genome-DBs/polyploidy/core/transcript_intron_supporting_evidence.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/transcript_supporting_feature.txt b/modules/t/test-genome-DBs/polyploidy/core/transcript_supporting_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/translation.txt b/modules/t/test-genome-DBs/polyploidy/core/translation.txt
new file mode 100644
index 0000000000..0ccbeaafe3
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/translation.txt
@@ -0,0 +1,6 @@
+79141 79141 1 243045 143 243046 Traes_6DS_3B68FB2E11.1 1 2014-01-21 14:05:47 2014-01-21 14:05:47
+79459 79459 23 243998 187 243998 Traes_6DS_F1A510F0D1.1 1 2014-01-21 14:05:48 2014-01-21 14:05:48
+80726 80726 1 247713 216 247713 Traes_6DS_262C704652.1 1 2014-01-21 14:05:56 2014-01-21 14:05:56
+116850 116850 150 357242 211 357243 Traes_5AL_7256A9F19.3 1 2014-01-21 14:17:38 2014-01-21 14:17:38
+123920 123920 1 379407 204 379407 Traes_6BS_5FDE5650B.1 1 2014-01-21 14:18:24 2014-01-21 14:18:24
+124987 124987 1 382466 243 382466 Traes_6BS_48A5D59CE.1 1 2014-01-21 14:18:30 2014-01-21 14:18:30
diff --git a/modules/t/test-genome-DBs/polyploidy/core/translation_attrib.txt b/modules/t/test-genome-DBs/polyploidy/core/translation_attrib.txt
new file mode 100644
index 0000000000..c96b970eee
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/translation_attrib.txt
@@ -0,0 +1,30 @@
+124987 166 9566.19
+124987 168 118.101
+124987 165 7.5
+124987 164 10.2248
+124987 167 81
+80726 166 8194.45
+80726 168 115.415
+80726 165 7.0
+80726 164 10.6220
+80726 167 71
+79459 168 116.792
+79459 165 0.5
+79459 164 7.5424
+79459 167 54
+79459 166 6306.76
+116850 165 2.5
+116850 164 6.8239
+116850 167 310
+116850 166 33595.74
+116850 168 108.373
+79141 166 12775.81
+79141 168 108.270
+79141 165 6.5
+79141 164 11.2305
+79141 167 118
+123920 167 68
+123920 164 5.5837
+123920 165 -1.0
+123920 168 117.178
+123920 166 7968.14
diff --git a/modules/t/test-genome-DBs/polyploidy/core/unmapped_object.txt b/modules/t/test-genome-DBs/polyploidy/core/unmapped_object.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/polyploidy/core/unmapped_reason.txt b/modules/t/test-genome-DBs/polyploidy/core/unmapped_reason.txt
new file mode 100644
index 0000000000..fae97f6f53
--- /dev/null
+++ b/modules/t/test-genome-DBs/polyploidy/core/unmapped_reason.txt
@@ -0,0 +1,51 @@
+1 Marker matches multiple times Marker aligns to the genome > 3 times
+2 Marker does not align Unable to align to the genome
+3 Failed to find Stable ID Stable ID that this xref was linked to no longer exists
+4 No mapping done No mapping done for this type of xref
+5 Failed to match Unable to match to any ensembl entity at all
+6 Failed to match at thresholds Unable to match at the thresholds of 90% for the query or 90% for the target
+7 No Master The dependent xref was not matched due to there being no master xref
+8 Master failed The dependent xref was not matched due to the master xref not being mapped
+40 Was not best match Did not top best transcript match score (0.75)
+41 Was not best match Did not top best transcript match score (0.76)
+42 Was not best match Did not top best transcript match score (0.77)
+43 Was not best match Did not top best transcript match score (0.78)
+44 Was not best match Did not top best transcript match score (0.79)
+45 Was not best match Did not top best transcript match score (0.80)
+46 Was not best match Did not top best transcript match score (0.81)
+47 Was not best match Did not top best transcript match score (0.82)
+48 Was not best match Did not top best transcript match score (0.83)
+49 Was not best match Did not top best transcript match score (0.84)
+50 Was not best match Did not top best transcript match score (0.85)
+51 Was not best match Did not top best transcript match score (0.86)
+52 Was not best match Did not top best transcript match score (0.87)
+53 Was not best match Did not top best transcript match score (0.88)
+54 Was not best match Did not top best transcript match score (0.89)
+55 Was not best match Did not top best transcript match score (0.90)
+56 Was not best match Did not top best transcript match score (0.91)
+57 Was not best match Did not top best transcript match score (0.92)
+58 Was not best match Did not top best transcript match score (0.93)
+59 Was not best match Did not top best transcript match score (0.94)
+60 Was not best match Did not top best transcript match score (0.95)
+61 Was not best match Did not top best transcript match score (0.96)
+62 Was not best match Did not top best transcript match score (0.97)
+63 Was not best match Did not top best transcript match score (0.98)
+64 Was not best match Did not top best transcript match score (0.99)
+65 Was not best match Did not top best transcript match score (1.00)
+66 Did not meet threshold Match score for transcript lower than threshold (0.75)
+67 No overlap No coordinate overlap with any Ensembl transcript
+96 Failed to match at thresholds Unable to match at the thresholds of 100% for the query or 100% for the target
+125 Failed to match at thresholds Unable to match at the thresholds of 55% for the query or 55% for the target
+126 >10% N-strings More than 10% of the sequence consists of strings of Ns. Sequences are not rejected for this reason but this may explain a low coverage hit
+127 All long introns Every intron in these hits is of length 250000-400000bp, we require at least one intron to be shorter than 250000bp
+128 GSS sequence This cDNA has been excluded from the analysis because it is in the GSS (Genome Survey Sequence) division of GenBank
+129 Low coverage Coverage of the best alignment is less than 90% - see query_score for coverage
+130 Low coverage with long intron Hits containing introns longer than 250000bp are rejected if coverage is less than 98% - see query_score for coverage
+131 Low percent_id with long intron Hits containing introns longer than 250000bp are rejected if percentage identity is less than 98% - see query_score for percent_id
+132 Low percent_id Percentage identity of the best alignment is less than 97% - see query_score for percent_id
+133 No output from Exonerate Exonerate returned no hits using standard parameters plus options --maxintron 400000 and --softmasktarget FALSE
+134 Parent xref failed to match Unable to match as parent xref was not mapped
+135 Processed pseudogene Rejected as a processed pseudogene because there are multiple-exon hits with the same coverage which have been rejected for other reasons
+136 See kill-list database This sequence has been excluded from the analysis - see the kill-list database for further details
+137 Failed to match at thresholds Unable to match at the thresholds of 99% for the query or 99% for the target
+138 Marker matches multiple times Marker aligns to the genome > 5 times
diff --git a/modules/t/test-genome-DBs/polyploidy/core/xref.txt b/modules/t/test-genome-DBs/polyploidy/core/xref.txt
new file mode 100644
index 0000000000..e69de29bb2
--
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