[ENSCORESW-1117]. Polyploidy test database extracted from Triticum aestivum (EG25).

modules/t/test-genome-DBs/polyploidy/core/analysis.txt

+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

modules/t/test-genome-DBs/polyploidy/core/analysis_description.txt

+178	<a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/27/2/573?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Benson&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/1999&amp;tdate=12/31/1999&amp;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&amp;_udi=B6TFV-44PXMF3-45&amp;_user=776054&amp;_coverDate=06%2F30%2F1993&amp;_rdoc=6&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%235236%231993%23999829997%23279143%23FLP%23display%23Volume)&amp;_cdi=5236&amp;_sort=d&amp;_docanchor=&amp;_ct=13&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Bateman&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Attwood&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=letunic&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2006&amp;tdate=12/31/2006&amp;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&amp;_udi=B6WK7-457D7V9-K&amp;_user=776054&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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&amp;_udi=B6WK7-4CKBS0M-3&amp;_user=776054&amp;_coverDate=07%2F16%2F2004&amp;_alid=772330061&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_ct=1&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Haft&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2003&amp;tdate=12/31/2003&amp;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&amp;_udi=B6WK7-457CXWM-3D&amp;_user=776054&amp;_coverDate=11%2F02%2F2001&amp;_rdoc=17&amp;_fmt=high&amp;_orig=browse&amp;_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&amp;_cdi=6899&amp;_sort=d&amp;_docanchor=&amp;_ct=17&amp;_acct=C000042238&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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

modules/t/test-genome-DBs/polyploidy/core/assembly.txt

+3495644	3309354	1	4562	1	4562	1
+3495727	3355688	1	18301	1	18301	1
+3495794	3116582	1	5428	1	5428	1

modules/t/test-genome-DBs/polyploidy/core/coord_system.txt

+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

modules/t/test-genome-DBs/polyploidy/core/density_type.txt

+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

modules/t/test-genome-DBs/polyploidy/core/exon.txt

+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