Commit 85b2c237 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

added data to test patch regions

parent d9894386
......@@ -158,3 +158,8 @@
162031 469283 31225243 31225346 1 0 2 1 1 ENSE00001109602 1 2004-12-06 12:00:00 2004-12-06 12:00:00
162032 469283 31222465 31222583 1 1 0 1 1 ENSE00001109601 1 2004-12-06 12:00:00 2004-12-06 12:00:00
162033 965899 10060 10405 1 0 0 1 1 ENSE00001109603 1 2004-12-06 12:00:00 2004-12-06 12:00:00
7296473 1000357922 950956 951162 1 -1 -1 1 1 ENSE00002629711 1 2011-11-11 09:57:43 2011-11-11 09:57:43
7296474 1000357922 954720 955100 1 -1 -1 1 1 ENSE00002624037 1 2011-11-11 09:57:43 2011-11-11 09:57:43
7296475 1000357922 970445 970836 -1 -1 -1 1 1 ENSE00002580842 1 2011-11-11 09:57:43 2011-11-11 09:57:43
7296476 1000357922 969827 970115 -1 -1 -1 1 1 ENSE00002621881 1 2011-11-11 09:57:43 2011-11-11 09:57:43
7296477 1000357922 969238 969286 -1 -1 -1 1 1 ENSE00002622269 1 2011-11-11 09:57:43 2011-11-11 09:57:43
......@@ -169,3 +169,8 @@
162031 21739 4
162032 21739 3
162033 21740 0
7296473 2047706 1
7296474 2047706 2
7296475 2047707 1
7296476 2047707 2
7296477 2047707 3
......@@ -18,3 +18,5 @@
18273 protein_coding 1282 469283 31166507 31196939 1 97759 ensembl KNOWN MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691] 1 21738 \N ENSG00000101367 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18274 protein_coding 1282 469283 31210077 31225346 1 0 ensembl NOVEL \N 1 21739 \N ENSG00000167097 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18275 protein_coding 1282 965899 10060 10405 1 0 ensembl NOVEL \N 1 21740 \N ENSG00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
633682 lincRNA 8405 1000357922 950956 955100 1 3894583 havana NOVEL \N 1 2047706 \N ENSG00000260856 1 2011-11-11 09:57:43 2011-11-11 09:57:43
633683 pseudogene 8405 1000357922 969238 970836 -1 3894591 havana KNOWN ribosomal protein L14 pseudogene 5 [Source:HGNC Symbol;Acc:37720] 1 2047707 \N ENSG00000261370 1 2011-11-11 09:57:43 2011-11-11 09:57:43
18256 10 This is a note on gene 18256
18259 10 Another note on gene 18259
633682 348 lincRNA
633682 142 48.11
633683 348 processed_pseudogene
633683 142 51.72
......@@ -30,3 +30,4 @@
251369 95 99 \N \N \N \N \N \N \N
253531 100 45 \N \N \N \N \N \N \N
253682 100 100 \N \N \N \N \N \N \N
16739090 97 99 590 1 1 588 588M 2922 0
......@@ -17,7 +17,6 @@
56 1 assembly.mapping clone|contig
57 1 assembly.mapping supercontig|contig
58 1 assembly.mapping chromosome:NCBI33|contig|clone
59 1 assembly.mapping chromosome:NCBI33|contig|supercontig
60 1 assembly.mapping supercontig|contig|clone
64 1 assembly.mapping chromosome:NCBI33#chunk
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
......@@ -34,3 +33,139 @@
79 \N patch patch_70_71_b.sql|mapping_set_index
80 \N patch patch_71_72_a.sql|schema_version
81 \N patch patch_71_72_b.sql|associated_xref
2047 1 xref.timestamp 2013-05-08 23:30:53
4 \N patch patch_52_53_c.sql|identity_xref_rename
5 \N patch patch_52_53_d.sql|drop_go_xref_index
2014 1 species.classification Haplorrhini
41 1 assembly.date 2009-02
43 1 genebuild.id 39
44 1 genebuild.start_date 2010-07-Ensembl
45 1 genebuild.initial_release_date 2011-04
46 1 genebuild.last_geneset_update 2013-04
68 1 marker.priority 80
62 1 genebuild.method full_genebuild
2048 1 assembly.mapping chromosome:NCBI33|supercontig
381 \N patch patch_53_54_a.sql|schema_version
382 \N patch patch_53_54_b.sql|widen_columns
383 \N patch patch_53_54_c.sql|identity_object_analysis_move
384 \N patch patch_54_55_a.sql|schema_version
385 \N patch patch_54_55_b.sql|add_go_xrefs_types
386 \N patch patch_54_55_c.sql|add_splicing_event_tables
387 \N patch patch_54_55_d.sql|add_dependent_xref_table
388 \N patch patch_54_55_e.sql|add_is_constitutive_column
392 \N patch patch_54_55_f.sql|coord_system.version_null
393 \N patch patch_54_55_h.sql|gene_archive.allow_for_\Ns
394 \N patch patch_54_55_g.sql|analysis_description.display_label_\NOT_N
1990 1 assembly.overlapping_regions 1
462 1 assembly.coverage_depth high
463 1 repeat.analysis dust
464 1 repeat.analysis repeatmask
465 1 repeat.analysis trf
2004 1 species.stable_id_prefix E\NS
513 \N patch patch_55_56_a.sql|schema_version
514 \N patch patch_55_56_b.sql|add_index_names
515 \N patch patch_55_56_c.sql|drop_oligo_tables_and_xrefs
516 \N patch patch_55_56_d.sql|add_index_to_splicing_event_feature
2038 1 genebuild.level toplevel
2039 1 transcriptbuild.level toplevel
2001 1 species.alias homo
2040 1 exonbuild.level toplevel
2041 1 repeat_featurebuild.level toplevel
2042 1 dna_align_featurebuild.level toplevel
2043 1 protein_align_featurebuild.level toplevel
2044 1 simple_featurebuild.level toplevel
2045 1 prediction_transcriptbuild.level toplevel
2046 1 prediction_exonbuild.level toplevel
1999 1 species.alias homo sapiens
1996 1 species.alias hsap
1994 1 species.alias human
650 \N patch patch_56_57_a.sql|schema_version
653 \N patch patch_56_57_b.sql|unmapped_object.typ_enum_tidy
654 \N patch patch_56_57_c.sql|external_db_type_enum
696 \N patch patch_56_57_d.sql|allow_meta_null
697 \N patch patch_56_57_e.sql|canonical_translations
698 \N patch patch_56_57_f.sql|simple_feature.display_label
2011 1 species.classification Hominoidea
744 \N patch patch_57_58_a.sql|schema_version
808 1 lrg lrg
2013 1 species.classification Simiiformes
800 \N patch patch_58_59_a.sql|schema_version
801 \N patch patch_58_59_b.sql|assembly_exception_exc_type_enum
802 \N patch patch_58_59_c.sql|splicing_event_attrib_type_id
803 \N patch patch_58_59_d.sql|object_xref_extend_index
805 \N patch patch_58_59_e.sql|meta_schema_type
972 \N patch patch_59_60_a.sql|schema_version
973 \N patch patch_59_60_b.sql|rename_go_xref_table
974 \N patch patch_59_60_c.sql|QC_fixes
975 \N patch patch_60_61_a.sql|schema_version
976 \N patch patch_60_61_b.sql|create_seq_region_synonym_table
977 \N patch patch_60_61_c.sql|rejig_object_xref_indexes
1008 \N patch patch_61_62_a.sql|schema_version
1009 \N patch patch_61_62_b.sql|synonym_field_extension
1010 \N patch patch_61_62_c.sql|db_name_db_release_idx
1011 \N patch patch_61_62_d.sql|remove_display_label_linkable
1018 1 genebuild.havana_datafreeze_date 2013-02-11
1024 1 removed_evidence_flag.uniprot_dbversion uniprot_2013_04
1025 1 removed_evidence_flag.ensembl_dbversion homo_sapiens_core_72_37
1026 \N patch patch_61_62_e.sql|seq_region_synonym_seq_region_idx
1039 \N patch patch_63_64_a.sql|schema_version
1040 \N patch patch_62_63_a.sql|schema_version
1041 \N patch patch_62_63_b.sql|indexing_changes
1042 \N patch patch_62_63_c.sql|remove_dbprimary_acc_linkable
1043 \N patch patch_63_64_b.sql|add_operons
1044 \N patch patch_63_64_c.sql|is_ref_added_to_alt_allele
1048 \N patch patch_63_64_d.sql|linkage_type change in ontology_xref
1060 \N patch patch_64_65_a.sql|schema_version
1061 \N patch patch_64_65_b.sql|merge_stable_id_with_object
1062 \N patch patch_64_65_c.sql|add_data_file
1063 \N patch patch_64_65_d.sql|add_checksum_info_type
1082 \N patch patch_65_66_a.sql|schema_version
1083 \N patch patch_65_66_b.sql|fix_external_db_id
1084 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
1085 \N patch patch_65_66_d.sql|add_index_to_ontology_xref_table
1087 \N patch patch_65_66_e.sql|fix_external_db_id_in_xref
1088 \N patch patch_65_66_f.sql|drop_default_values
1184 \N patch patch_66_67_a.sql|schema_version
1185 \N patch patch_66_67_b.sql|drop_stable_id_views
1186 \N patch patch_66_67_c.sql|adding_intron_supporting_evidence
1187 \N patch patch_66_67_d.sql|adding_gene_transcript_annotated
1188 \N patch patch_66_67_e.sql|index_canonical_transcript_id
2027 1 species.classification Craniata
1562 1 assembly.web_accession_source NCBI
1563 1 assembly.web_accession_type GenBank Assembly ID
1997 1 species.alias homsap
2007 1 species.display_name Human
2037 1 species.url Homo_sapiens
2018 1 species.classification Theria
1718 \N patch patch_67_68_e.sql|fix_67_68_e_xref_index
1666 \N patch patch_67_68_a.sql|schema_version
1667 \N patch patch_67_68_b.sql|xref_uniqueness
1668 \N patch patch_67_68_c.sql|altering_intron_supporting_evidence
1669 \N patch patch_67_68_d.sql|add_is_splice_canonical_and_seq_index
2002 1 species.alias enshs
2025 1 species.classification Gnathostomata
2022 1 species.classification Sarcopterygii
1728 \N patch patch_68_69_a.sql|schema_version
1995 1 species.alias 9606
2020 1 species.classification Amniota
2021 1 species.classification Tetrapoda
1815 \N patch patch_69_70_a.sql|schema_version
1816 \N patch patch_69_70_b.sql|add_mapping_set_history
1817 \N patch patch_69_70_c.sql|column_datatype_consistency
1818 \N patch patch_69_70_d.sql|data_file_id_auto_increment
1819 \N patch patch_69_70_e.sql|protein_feature_hit_description
2000 1 species.alias homo_sapiens
1998 1 species.alias hsapiens
2009 1 species.classification Homininae
1904 \N patch patch_70_71_a.sql|schema_version
1905 \N patch patch_70_71_b.sql|mapping_set_index
2024 1 species.classification Teleostomi
2023 1 species.classification Euteleostomi
2016 1 species.classification Euarchontoglires
1991 \N patch patch_71_72_a.sql|schema_version
1992 \N patch patch_71_72_b.sql|associated_xref
2003 1 species.alias h_sapiens
2029 1 species.classification Deuterostomia
2030 1 species.classification Bilateria
2031 1 species.classification Eumetazoa
2033 1 species.classification Opisthokonta
......@@ -22,3 +22,8 @@ regulatory_feature 1 121
regulatory_search_region 1 121
operon 1 106713
operon_transcript 1 106713
gene 2 4145
exon 2 392
dna_align_feature 2 383
transcript 2 730
protein_align_feature 2 354
......@@ -203,3 +203,20 @@
253682 21727 Translation 168444 119 0
253683 21727 Translation 168445 119 0
253684 21727 Translation 168446 119 0
16739087 633682 Gene 3894581 \N 8406
16739088 633682 Gene 3894582 \N 0
16739089 633682 Gene 3894583 \N 8406
16739090 633682 Gene 3894584 \N 8406
16739091 2047706 Transcript 3894585 \N 0
16739092 2047706 Transcript 3894586 \N 0
16739093 2047706 Transcript 3894587 \N 0
16739094 2047706 Transcript 3894588 \N 8406
16739095 633683 Gene 3894589 \N 8406
16739096 633683 Gene 3894590 \N 0
16739097 633683 Gene 3894591 \N 8406
16739098 2047707 Transcript 3894592 \N 0
16739099 2047707 Transcript 3894593 \N 0
16739100 2047707 Transcript 3894594 \N 0
16739101 2047707 Transcript 3894595 \N 8406
16739102 2047707 Transcript 3894591 \N 8406
16739103 2047707 Transcript 3894596 \N 8406
......@@ -7232,3 +7232,10 @@
2161556 469270 39321 39326 -1 1521 1522 Q9UHA8 5 149 4.4e-06 29 6M \N \N
2161596 469270 39321 39323 -1 279 279 Q94IK7 5 133 1.3e-05 26 3M \N \N
2161649 469270 39321 39323 -1 366 366 Q9Q5L3 5 123 0.00058 27 3M \N \N
19573204 1000357922 970483 970836 -1 1 118 P50914.4 8408 465 1.8e-43 77 354M 2200 0
19573205 1000357922 970483 970836 -1 1 118 Q63507.3 8408 455 9.5e-48 73 354M 2200 0
19573206 1000357922 970483 970836 -1 1 118 Q9CR57.3 8408 452 1.1e-46 72 354M 2200 0
19573207 1000357922 969860 969970 -1 167 205 P50914.4 8408 60 1.8e-43 52 12M6D39M3I33M3D24M 2200 0
19573208 1000357922 970114 970149 -1 130 141 P50914.4 8408 51 1.8e-43 91 36M 2200 0
19573209 1000357922 970114 970149 -1 130 141 Q63507.3 8408 48 1.5e-39 83 36M 2200 0
19573210 1000357922 970114 970149 -1 130 141 Q9CR57.3 8408 46 4.9e-39 75 36M 2200 0
......@@ -95,3 +95,8 @@
965888 AF347015.1.1.16571 4 16571
965905 multimap_testregion 6 1000
965906 gap_map_test 7 10000
24403 AL672311.26 1 115998
26504 BX649635.3 1 43709
1000357922 HG480_HG481_PATCH 1 155131142
1000357923 HG480_HG481_PATCH 2 284527
1000357972 AL672277.21 4 131682
......@@ -14,3 +14,15 @@
965899 17 2
965888 17 2
469351 18 1
27516 367 23
27516 6 1
27516 10 2295302
27516 353 735
27516 67 838
27516 64 833
1000357922 16 1
1000357922 312 2011-07-01 15:44:52
1000357922 6 1
1000357922 369 833
1000357922 370 838
1000357922 368 735
......@@ -328,3 +328,11 @@
162030 dna_align_feature 29498396
162031 dna_align_feature 29498395
162032 dna_align_feature 29498394
7296474 dna_align_feature 29385292
7296475 protein_align_feature 19573204
7296475 protein_align_feature 19573205
7296475 protein_align_feature 19573206
7296476 protein_align_feature 19573207
7296476 protein_align_feature 19573208
7296476 protein_align_feature 19573209
7296476 protein_align_feature 19573210
......@@ -23,3 +23,4 @@
21738 18273 1282 469283 31166507 31196939 1 97759 protein_coding KNOWN \N 1 21738 ENST00000217347 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21739 18274 1282 469283 31210077 31225346 1 0 protein_coding NOVEL \N 1 21739 ENST00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 18275 1282 965899 10060 10405 1 0 protein_coding NOVEL \N 1 21740 ENST00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
2047706 633682 8405 1000357922 950956 955100 1 3894588 lincRNA KNOWN \N 1 0 ENST00000568661 1 2011-11-11 09:57:43 2011-11-11 09:57:43
2047706 4 RP11-309M23.1-001
2047706 52 Havana
2047706 53 vega@sanger.ac.uk
2047707 4 RP11-309M23.2-001
2047707 52 Havana
2047707 53 vega@sanger.ac.uk
2047707 54 ribosomal protein L14 (RPL14) pseudogene
......@@ -183,3 +183,19 @@
103298 3 CAB53072 CAB53072 1 description D
999998 11 IPR000001 IPR000001 1 Test interpro desc1 D
999999 11 IPR000010 IPR000010 1 Test interpro desc2 D
3894581 20046 ENSG00000260856 ENSG00000260856 0 DIRECT
3894582 4600 OTTHUMG00000174632 OTTHUMG00000174632 1 N NONE
3894583 12310 RP11-309M23.1 RP11-309M23.1 0 N MISC via havana clone name
3894584 4100 Hs.512470 Hs.512470 0 Transcribed locus SEQUENCE_MATCH
3894585 2310 OTTHUMT00000427109 RP11-309M23.1-001 1 N NONE
3894586 2310 OTTHUMT00000427109 OTTHUMT00000427109 1 N NONE Added during ensembl-vega production
3894587 4610 OTTHUMT00000427109 OTTHUMT00000427109 1 N NONE
3894588 12410 RP11-309M23.1-001 RP11-309M23.1-001 0 DIRECT
3894589 20046 ENSG00000261370 ENSG00000261370 0 DIRECT
3894590 4600 OTTHUMG00000174633 OTTHUMG00000174633 1 N NONE
3894591 1100 37720 RPL14P5 0 ribosomal protein L14 pseudogene 5 DIRECT Generated via ensembl_manual
3894592 2310 OTTHUMT00000427110 RP11-309M23.2-001 1 N NONE
3894593 2310 OTTHUMT00000427110 OTTHUMT00000427110 1 N NONE Added during ensembl-vega production
3894594 4610 OTTHUMT00000427110 OTTHUMT00000427110 1 N NONE
3894595 12410 RP11-309M23.2-001 RP11-309M23.2-001 0 DIRECT
3894596 50609 RPL14P5-001 RPL14P5-001 0 ribosomal protein L14 pseudogene 5 MISC
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