Schema for Alt Haplotypes - Reference Assembly Alternate Haplotype Sequence Alignments
  Database: mm10    Primary Table: altSeqLiftOverPsl    Row Count: 22   Data last updated: 2021-05-12
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 16smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 262068int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1380int(10) unsigned range Number of bases that don't match
repMatches 148387int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 202int(10) unsigned range Number of inserts in query
qBaseInsert 44963int(10) unsigned range Number of bases inserted in query
tNumInsert 206int(10) unsigned range Number of inserts in target
tBaseInsert 10499int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName chr1_KK082441_altvarchar(255) values Query sequence name
qSize 456798int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 456798int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 195471971int(10) unsigned range Target sequence size
tStart 60694704int(10) unsigned range Alignment start position in target
tEnd 61117038int(10) unsigned range Alignment end position in target
blockCount 408int(10) unsigned range Number of blocks in alignment
blockSizes 1351,2131,41,1007,479,2288,...longblob   Size of each block
qStarts 0,1351,3482,3533,4540,5031,...longblob   Start of each block in query.
tStarts 60694704,60696069,60698208,...longblob   Start of each block in target.

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
16262068138014838702024496320610499+chr1_KK082441_alt4567980456798chr119547197160694704611170384081351,2131,41,1007,479,2288,1510,125,55,359,5,1143,819,64,207,829,466,439,3482,4230,289,52,2005,69,2,1627,612,1797,569,600,2859,9 ...0,1351,3482,3533,4540,5031,7321,8831,8956,9011,9370,9375,10519,11340,11404,11707,14819,20834,21274,24757,28987,29276,29335,31340 ...60694704,60696069,60698208,60698249,60699257,60699736,60702024,60703675,60703843,60705706,60706072,60706080,60707223,60708042,60 ...
119106717137492881680142867971252+chr11_KZ289073_alt2152640215264chr1112208254348845020491172501544101,1510,7,975,1523,1399,2839,181,39,67,1426,1458,1196,164,3381,1779,3560,1380,1390,2276,253,979,1463,841,1054,54,2021,2825,26, ...0,4105,5615,5622,6604,8127,9526,12366,12549,12599,12666,14092,15550,16746,16910,20291,22091,25651,27032,28422,30698,30951,31934, ...48845020,48849121,48850634,48850643,48851618,48853159,48854559,48857398,48857579,48857618,48857695,48859125,48860587,48861784,48 ...
11993636252158670017131317156117443+chr11_KZ289077_alt1861440186144chr1112208254348845231491175013201388,367,1411,2223,964,1546,4420,40,24,35,4265,3400,1762,158,263,620,703,1007,371,116,284,171,550,11,649,3914,63,585,78,217,2108 ...0,1389,1756,3168,5391,6355,7901,12322,12362,12386,12442,16707,20115,21898,22057,22320,22944,23650,24657,25032,25148,25435,25609, ...48845231,48846619,48846989,48848400,48850626,48851595,48853159,48857579,48857621,48857648,48857683,48861950,48865350,48867112,48 ...
171004563111145790018414562521037860+chr11_KZ289080_alt3949820394982chr111220825437104950771336724390386,243,40,102,341,140,787,1285,198,3159,505,254,80,785,57,68,61,97,37,84,3,30,7,30,34,7,10,8,14,80,517,365,252,40,406,107,64,19 ...0,398,652,700,802,1143,1311,2099,3384,3582,6825,7336,7590,7671,9129,9186,9256,9318,9416,9453,9538,9541,9572,9580,9611,9646,9653, ...71049507,71049893,71050136,71050176,71050279,71050621,71050761,71051548,71052834,71053033,71056192,71056697,71056955,71057035,71 ...
140895861865115130212718433713119995+chr11_KZ289078_alt3909200390920chr1112208254371073520713000982561914,1215,2206,3894,2529,9196,2817,13,38,98,103,3153,264,1820,1446,1143,2967,443,63,860,2,918,57,140,122,336,2749,1132,94,572,32 ...0,1915,3130,5337,9231,13278,22474,25306,25320,25378,25478,25582,28735,28999,30819,32265,33408,36375,36818,36881,37742,37749,3867 ...71073520,71075434,71076650,71078856,71082751,71085280,71094493,71097310,71097323,71097361,71097459,71097562,71100716,71100984,71 ...
1776721654582049033822871130369086+chr11_KZ289074_alt3940260394026chr1112208254371074360713087616308390,3793,1456,9321,1153,12183,658,4554,3295,3778,6036,1499,1255,9502,55,2159,792,699,125,312,1979,310,2469,77,2509,2321,1512,24 ...0,8390,12186,13642,22963,24117,36302,36960,41514,44809,48588,54624,56124,57383,66885,66941,69100,69892,70591,70742,71054,73033,7 ...71074360,71082751,71086544,71088001,71097326,71098479,71110662,71111321,71115877,71119173,71122951,71128988,71130487,71131742,71 ...
152175601386117633603231416632361317+chr11_KZ289081_alt3699739369973chr111220825438293346383350578641568,841,569,28,755,34,411,362,1873,1017,922,2142,57,1282,393,38,596,481,375,750,525,424,959,570,1147,973,304,271,603,847,1180,46 ...9,578,1419,1988,2016,2795,2829,3240,3603,5476,6493,7439,9584,9645,10964,11357,11399,11995,12477,12852,13610,14135,14559,15518,16 ...82933463,82934031,82934876,82935487,82935521,82936276,82936311,82936726,82937088,82938963,82939981,82940903,82943045,82943102,82 ...
152177160311017781902471081227761045+chr11_KZ289079_alt3689670368901chr111220825438293466383353797520773,590,224,812,3379,436,48,2091,27,195,1076,478,596,493,367,123,668,433,45,424,974,606,2067,304,272,603,2021,469,211,162,1654,4 ...0,773,1367,1595,2408,5791,6237,6285,8378,8405,8600,9685,10167,10763,11258,11625,11748,12416,12849,12894,13318,14292,14898,16967, ...82934663,82935462,82936052,82936276,82937088,82940467,82940903,82940952,82943043,82943071,82943267,82944343,82944821,82945425,82 ...
15214505716061685810111697214548416+chr11_KZ289075_alt3222210322216chr111220825438293499983298659254449,11,531,240,729,67,234,1638,122,1806,2141,25,1278,428,38,596,1651,479,428,967,609,2066,304,272,603,844,1668,195,636,1176,501, ...0,449,460,995,1247,1980,2048,2287,3925,4047,5867,8011,8036,9345,9773,9815,10411,12062,12541,12969,13936,14545,16612,16916,17188, ...82934999,82935498,82935521,82936052,82936292,82937021,82937088,82937322,82938961,82939098,82940904,82943045,82943071,82944349,82 ...
73106717137492881679712528014286+chr111220825434884502049117250chr11_KZ289073_alt21526402152641544101,1510,7,975,1523,1399,2839,181,39,67,1426,1458,1196,164,3381,1779,3560,1380,1390,2276,253,979,1463,841,1054,54,2021,2825,26, ...48845020,48849121,48850634,48850643,48851618,48853159,48854559,48857398,48857579,48857618,48857695,48859125,48860587,48861784,48 ...0,4105,5615,5622,6604,8127,9526,12366,12549,12599,12666,14092,15550,16746,16910,20291,22091,25651,27032,28422,30698,30951,31934, ...

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Alt Haplotypes (altSeqLiftOverPsl) Track Description
 

Description

This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted in red. Several types of alignment gap may also be colored; for more information, see Alignment Insertion/Deletion Display Options.

Credits

The alignments were provided by NCBI as GFF files and translated into the PSL representation for browser display by UCSC.