259 lines
17 KiB
Text
259 lines
17 KiB
Text
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<!DOCTYPE html>
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<html>
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<title>Mouse genome issues - Genome Reference Consortium</title>
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<script>
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var taxid = "10090",
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chromosomes = {'GRCm39': {'1': {'name': '1', 'length': 195154279, 'genbank': 'CM000994.3', 'refseq': 'NC_000067.7', 'canonical': 'NC_000067.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '2': {'name': '2', 'length': 181755017, 'genbank': 'CM000995.3', 'refseq': 'NC_000068.8', 'canonical': 'NC_000068.8', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '3': {'name': '3', 'length': 159745316, 'genbank': 'CM000996.3', 'refseq': 'NC_000069.7', 'canonical': 'NC_000069.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '4': {'name': '4', 'length': 156860686, 'genbank': 'CM000997.3', 'refseq': 'NC_000070.7', 'canonical': 'NC_000070.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '5': {'name': '5', 'length': 151758149, 'genbank': 'CM000998.3', 'refseq': 'NC_000071.7', 'canonical': 'NC_000071.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '6': {'name': '6', 'length': 149588044, 'genbank': 'CM000999.3', 'refseq': 'NC_000072.7', 'canonical': 'NC_000072.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '7': {'name': '7', 'length': 144995196, 'genbank': 'CM001000.3', 'refseq': 'NC_000073.7', 'canonical': 'NC_000073.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '8': {'name': '8', 'length': 130127694, 'genbank': 'CM001001.3', 'refseq': 'NC_000074.7', 'canonical': 'NC_000074.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '9': {'name': '9', 'length': 124359700, 'genbank': 'CM001002.3', 'refseq': 'NC_000075.7', 'canonical': 'NC_000075.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '10': {'name': '10', 'length': 130530862, 'genbank': 'CM001003.3', 'refseq': 'NC_000076.7', 'canonical': 'NC_000076.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '11': {'name': '11', 'length': 121973369, 'genbank': 'CM001004.3', 'refseq': 'NC_000077.7', 'canonical': 'NC_000077.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '12': {'name': '12', 'length': 120092757, 'genbank': 'CM001005.3', 'refseq': 'NC_000078.7', 'canonical': 'NC_000078.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '13': {'name': '13', 'length': 120883175, 'genbank': 'CM001006.3', 'refseq': 'NC_000079.7', 'canonical': 'NC_000079.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '14': {'name': '14', 'length': 125139656, 'genbank': 'CM001007.3', 'refseq': 'NC_000080.7', 'canonical': 'NC_000080.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '15': {'name': '15', 'length': 104073951, 'genbank': 'CM001008.3', 'refseq': 'NC_000081.7', 'canonical': 'NC_000081.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '16': {'name': '16', 'length': 98008968, 'genbank': 'CM001009.3', 'refseq': 'NC_000082.7', 'canonical': 'NC_000082.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '17': {'name': '17', 'length': 95294699, 'genbank': 'CM001010.3', 'refseq': 'NC_000083.7', 'canonical': 'NC_000083.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '18': {'name': '18', 'length': 90720763, 'genbank': 'CM001011.3', 'refseq': 'NC_000084.7', 'canonical': 'NC_000084.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '19': {'name': '19', 'length': 61420004, 'genbank': 'CM001012.3', 'refseq': 'NC_000085.7', 'canonical': 'NC_000085.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, 'X': {'name': 'X', 'length': 169476592, 'genbank': 'CM001013.3', 'refseq': 'NC_000086.8', 'canonical': 'NC_000086.8', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, 'Y': {'name': 'Y', 'length': 91455967, 'genbank': 'CM001014.3', 'refseq': 'NC_000087.8', 'canonical': 'NC_000087.8', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}}, 'GRCm38.p6': {'1': {'name': '1', 'length': 195471971, 'genbank': 'CM000994.2', 'refseq': 'NC_000067.6', 'canonical': 'NC_000067.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '2': {'name': '2', 'length': 182113224, 'genbank': 'CM000995.2', 'refseq': 'NC_000068.7', 'canonical': 'NC_000068.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '3': {'name': '3', 'length': 160039680, 'genbank': 'CM000996.2', 'refseq': 'NC_000069.6', 'canonical': 'NC_000069.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '4': {'name': '4', 'length': 156508116, 'genbank': 'CM000997.2', 'refseq': 'NC_000070.6', 'canonical': 'NC_000070.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '5': {'name': '5', 'length': 151834684, 'genbank': 'CM000998.2', 'refseq': 'NC_000071.6', 'canonical': 'NC_000071.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '6': {'name': '6', 'length': 149736546, 'genbank': 'CM000999.2', 'refseq': 'NC_000072.6', 'canonical': 'NC_000072.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '7': {'name': '7', 'length': 145441459, 'genbank': 'CM001000.2', 'refseq': 'NC_000073.6', 'canonical': 'NC_000073.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '8': {'name': '8', 'length': 129401213, 'genbank': 'CM001001.2', 'refseq': 'NC_000074.6', 'canonical': 'NC_000074.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '9': {'name': '9', 'length': 124595110, 'genbank': 'CM001002.2', 'refseq': 'NC_000075.6', 'canonical': 'NC_000075.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '10': {'name': '10', 'length': 130694993, 'genbank': 'CM001003.2', 'refseq': 'NC_000076.6', 'canonical': 'NC_000076.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '11': {'name': '11', 'length': 122082543, 'genbank': 'CM001004.2', 'refseq': 'NC_000077.6', 'canonical': 'NC_000077.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '12': {'name': '12', 'length': 120129022, 'genbank': 'CM001005.2', 'refseq': 'NC_000078.6', 'canonical': 'NC_000078.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '13': {'name': '13', 'length': 120421639, 'genbank': 'CM001006.2', 'refseq': 'NC_000079.6', 'canonical': 'NC_000079.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '14': {'name': '14', 'length': 124902244, 'genbank': 'CM001007.2', 'refseq': 'NC_000080.6', 'canonical': 'NC_000080.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '15': {'name': '15', 'length': 104043685, 'genbank': 'CM001008.2', 'refseq': 'NC_000081.6', 'canonical': 'NC_000081.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '16': {'name': '16', 'length': 98207768, 'genbank': 'CM001009.2', 'refseq': 'NC_000082.6', 'canonical': 'NC_000082.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '17': {'name': '17', 'length': 94987271, 'genbank': 'CM001010.2', 'refseq': 'NC_000083.6', 'canonical': 'NC_000083.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '18': {'name': '18', 'length': 90702639, 'genbank': 'CM001011.2', 'refseq': 'NC_000084.6', 'canonical': 'NC_000084.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, '19': {'name': '19', 'length': 61431566, 'genbank': 'CM001012.2', 'refseq': 'NC_000085.6', 'canonical': 'NC_000085.6', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, 'X': {'name': 'X', 'length': 171031299, 'genbank': 'CM001013.2', 'refseq': 'NC_000086.7', 'canonical': 'NC_000086.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}, 'Y': {'name': 'Y', 'length': 91744698, 'genbank': 'CM001014.2', 'refseq': 'NC_000087.7', 'canonical': 'NC_000087.7', 'canonical_db_name': 'RefSeq', 'type': 'chromosome'}}},
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assemblies = [{'name': 'GRCm39', 'type': 'Major', 'gb_acc': 'GCA_000001635.9', 'rs_acc': 'GCF_000001635.27', 'accessions': {'genBank': 'GCA_000001635.9', 'refSeq': 'GCF_000001635.27'}, 'release_date': '2020-06-24', 'pretty_release_date': 'June 24, 2020', 'release_notes': 'GRCm39 is the second major update to the mouse reference assembly released by the GRC. All chromosome coordinates have changed, and more than 370 reported issues have been resolved. The chromosome sequences continue to represent the C57BL/6J strain, but the assembly no longer includes alternate loci scaffolds representing genomic regions from other strains.', 'group': '15', 'ftp_path': 'GCA/000/001/635/GCA_000001635.9_GRCm39'}, {'name': 'GRCm38.p6', 'type': 'Patch', 'gb_acc': 'GCA_000001635.8', 'rs_acc': 'GCF_000001635.26', 'accessions': {'genBank': 'GCA_000001635.8', 'refSeq': 'GCF_000001635.26'}, 'release_date': '2017-09-15', 'pretty_release_date': 'September 15, 2017', 'release_notes': 'Minor update of the assembly. 24 new FIX patches, 2 updated FIX patches and 8 new NOVEL patches. The total number of patch scaffolds is now 65 FIX and 9 NOVEL.', 'group': '15', 'ftp_path': 'GCA/000/001/635/GCA_000001635.8_GRCm38.p6'}, {'name': 'MGSCv37', 'type': 'Major', 'gb_acc': 'GCA_000001635.1', 'rs_acc': 'GCF_000001635.18', 'accessions': {'genBank': 'GCA_000001635.1', 'refSeq': 'GCF_000001635.18'}, 'release_date': '2010-09-23', 'pretty_release_date': 'September 23, 2010', 'release_notes': 'Last assembly released by the MGSC. The GRC has updated the assembly structure so that it resembles human. This means the alternate loci (sequence from other strains) have been aligned to the chromosome and put into a chromosome context. Some alternate loci that were very similar to C57BL/6J were dropped, but no changes were made to the C57BL/6J part of the assemlby. This assembly was also submitted to GenBank.', 'group': '15', 'ftp_path': 'GCA/000/001/635/GCA_000001635.1_MGSCv37'}], // Assemblies that have issue mappings for this organism
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asmAcc = "",
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asmName = "GRCm39",
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organism = {'taxid': '10090', 'common_name': 'Mouse', 'common_name_lowercase': 'mouse', 'scientific_name': 'Mus musculus'},
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uncuratedChromosomes = [];
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</script>
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<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/issues/filter-data-django.js?d=20150303"></script>
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<b>Warning:</b> this web site requires JavaScript to function. <a href="/guide/browsers#js_settings">more...</a>
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<img alt="GRC logo" src="/grc/static/grc/img/GRC_logo_reasonably_small.png" /><img src="/grc/static/grc/img/TitleBanner.png" alt="Genome Reference Consortium" /></a>
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<li><a href="/grc/mouse/issues" id="issueListMenuItem">Mouse Genome Issues</a></li>
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<h1>Mouse Genome Issues</h1>
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<div id="pick-assembly" class="gb-section">
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<h4><span id="pick-assembly-label">Show issue locations on</span></h4>
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<select id="assembly-select">
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<option>GRCm39</option>
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<option>GRCm38.p6</option>
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<option>MGSCv37</option>
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<i>Examples</i>
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<ul id="examples">
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<li class="gene-example">Gene: <a href="?q=Sirt2">Sirt2</a></li>
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<li class="location-example">Location: <a href="?q=chr7:35000000-9000000">chr7:3,500,000-9,000,000</a></li>
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<li class="clone-accession-example">Clone accession: <a href="?q=AC133487.14">AC133487.14</a></li>
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<li class="clone-name-example">Clone name: <a href="?q=RP23-8D10">RP23-8D10</a></li>
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</div> --!>
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<th id="issue-id-column-header">Issue ID</th>
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<th id="type-column-header">Type</th>
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<!-- <th id="region-column-header">Region</th> -->
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<th id="location-column-header">Location</th>
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<th id="total-placements-column-header">Total placements</th>
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<th id="status-column-header">Status</th>
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<!-- <th id="resolution-column-header">Resolution</th> -->
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<!-- <th id="affects-column-header">Affects version</th> -->
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<th id="fix-column-header" >Fix version</th>
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<!-- <th id="scaffold-type-column-header">Scaffold type</th> -->
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<th id="summary-column-header">Summary</th>
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<script type="text/javascript">
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if (typeof issues == "undefined") {
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// Recovery mechanism for when filter-data.js cannot be found
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$.ajax({
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url: "?org=mouse&no-cache=1&format=js",
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<li><a title="Get GRC data via FTP" href="https://ftp.ncbi.nlm.nih.gov/pub/grc/">FTP</a></li>
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<li><a target="_blank" href="https://www.genome.gov">NHGRI</a></li>
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<li class="last"><a target="_blank" href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html">HHS Vulnerability Disclosure</a></li>
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</body>
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</html>
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