Schema for Alt Haplotypes - Reference Assembly Alternate Haplotype Sequence Alignments
  Database: hg38    Primary Table: altSeqLiftOverPsl    Row Count: 680   Data last updated: 2018-11-07
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 75smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 240995int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1286int(10) unsigned range Number of bases that don't match
repMatches 52311int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 31int(10) unsigned range Number of inserts in query
qBaseInsert 59852int(10) unsigned range Number of bases inserted in query
tNumInsert 57int(10) unsigned range Number of inserts in target
tBaseInsert 47868int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName chr1_KI270762v1_altvarchar(255) values Query sequence name
qSize 354444int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 354444int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 2448810int(10) unsigned range Alignment start position in target
tEnd 2791270int(10) unsigned range Alignment end position in target
blockCount 88int(10) unsigned range Number of blocks in alignment
blockSizes 181010,4993,16,8418,4353,18...longblob   Size of each block
qStarts 0,181010,186003,186019,1944...longblob   Start of each block in query.
tStarts 2448810,2629823,2634821,263...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg38.chromInfo.chrom (via altSeqLiftOverPsl.qName)
      hg38.extNcbiAltSequence.name (via altSeqLiftOverPsl.qName)
      hg38.seqNcbiAltSequence.acc (via altSeqLiftOverPsl.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
75240995128652311031598525747868+chr1_KI270762v1_alt3544440354444chr12489564222448810279127088181010,4993,16,8418,4353,1806,28,41,78,41,40,40,42,9,30,78,82,40,41,37,38,46,117,42,77,9,79,72,22,7,22,28,103,21,39,41,37,5,113, ...0,181010,186003,186019,194438,198791,210416,210444,210485,210563,210604,210644,210684,210726,210735,210765,210843,210925,210965, ...2448810,2629823,2634821,2635234,2643652,2648006,2649812,2649841,2649883,2649962,2650004,2650045,2650086,2650129,2650139,2650170, ...
851309383401472080271731929933+chr1_KQ983255v1_alt2786590278659chr1248956422130043841331280347175567,850,846,75,862,516,7758,76,92,31,649,798,302,6,339,1507,1609,77,208,325,989,4,182,344,160,433,624,700,173,168,1291,514,24 ...0,175567,176417,177264,177339,178201,178717,186477,186553,186645,186676,187325,188132,188435,188444,188783,190348,191959,192038, ...13004384,13179952,13180808,13181654,13181730,13182597,13183115,13190873,13190951,13220888,13220920,13221570,13222368,13222670,13 ...
85109697558125212034172202224+chr1_KI270766v1_alt25627120632256271chr12489564221307511213312803551058,336,4501,4740,3509,2328,5057,2048,698,2068,2,5077,12667,10893,5065,2327,8225,4516,2017,2115,1366,4165,2389,4163,398,1384,12 ...20632,21690,22027,26543,31283,34792,37144,42202,44253,44952,47020,47022,52103,64771,75665,80778,83105,91345,95862,97883,99998,10 ...13075112,13076172,13076508,13081009,13085750,13089274,13091602,13096659,13098707,13099405,13101480,13101483,13106560,13119227,13 ...
9516110821181331057478514+chr1_KQ458383v1_alt3499380349938chr124895642223237485235799591112870,5676,716,2482,329,8299,1483,1581,2549,3851,302624,0,12871,18547,19263,21746,22075,30374,31857,33440,35990,47314,23237485,23250355,23256034,23256758,23259240,23259570,23267870,23269354,23270935,23273484,23277335,
1252503731078060125754825+chr1_KZ208904v1_alt1661360166136chr1248956422282063562836676321130836,957,13821,280,1272,168,1032,686,1790,808,1063,1544,445,1711,105,900,166,468,458,1603,269,0,130837,131797,145618,145899,152903,153073,154105,154795,156586,157394,158457,160001,160446,162158,162263,163166,163332,163801, ...28206356,28337192,28338149,28351971,28352251,28353523,28353691,28354727,28355413,28357203,28358025,28359089,28360634,28361081,28 ...
12455861065859106524513128+chr1_KI270760v1_alt1095280109528chr124895642230352190304566011823343,5,4,88,54,59,1204,553,15703,288,67,8215,125,919,149,2621,253,50633,0,23343,23348,23352,23440,23495,23557,24761,25314,41017,41306,41374,49589,49714,50633,50782,55006,58895,30352190,30375552,30375581,30375596,30375685,30375739,30375798,30377009,30377567,30393271,30393559,30393626,30401842,30401971,30 ...
17495821681789038968510+chr1_KZ208905v1_alt1403550140355chr12489564227228773372419130941617,1408,3913,2559,384,2192,2892,1877,74545,0,41617,43028,46941,49508,49892,61041,63933,65810,72287733,72329353,72330761,72334676,72337235,72337620,72339812,72342705,72344585,
172552954680388045290312+chr1_KQ458382v1_alt1410190141019chr124895642210390938010404512184043,17310,696,6179,617,2062,1744,103078,0,4043,21353,22051,28238,34134,36196,37941,103909380,103913427,103930739,103931435,103937614,103938231,103940299,103942043,
2112389133117765203624914631249726+chr1_KV880763v1_alt5510200551020chr124895642210798782410853942466126194,711,551,1226,4877,1642,186,3848,1430,10021,2273,10150,3103,147,411,1319,2749,759,3713,1600,642,5,1650,11087,2455,1,525,13 ...0,126194,126907,127458,128684,133561,135203,135389,139238,140668,150691,152964,163133,166241,166389,166801,168120,170869,171632, ...107987824,108114024,108114735,108115287,108116514,108121410,108123058,108123245,108127093,108128525,108138546,108140820,10815097 ...
1769281156115533404910252435-chr1_KV880763v1_alt551020234766483574chr124895642210822260110847174210254,42,46,1757,3759,6608,196,9878,1013,518,1144,192,146,4707,1389,1753,690,1231,775,7506,104,6680,943,3588,2474,294,35,14055,9272 ...67446,67501,67543,67590,69347,73106,79714,79911,89789,90803,91326,92470,92664,92811,97519,98908,100661,101351,102582,103357,1108 ...108222601,108222655,108222698,108222744,108224502,108228262,108234871,108235067,108244963,108245976,108246494,108247639,10824783 ...

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.