Schema for Alt Haplotypes - Reference Assembly Alternate Haplotype Sequence Alignments |
|---|
| |
Database: hg38 Primary Table: altSeqLiftOverPsl Row Count: 738 Data last updated: 2022-11-04
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
|---|
| bin | 75 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 240995 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 1286 | int(10) unsigned | range | Number of bases that don't match |
| repMatches | 52311 | int(10) unsigned | range | Number of bases that match but are part of repeats |
| nCount | 0 | int(10) unsigned | range | Number of 'N' bases |
| qNumInsert | 31 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 59852 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 57 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 47868 | int(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_alt | varchar(255) | values | Query sequence name |
| qSize | 354444 | int(10) unsigned | range | Query sequence size |
| qStart | 0 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 354444 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 248956422 | int(10) unsigned | range | Target sequence size |
| tStart | 2448810 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 2791270 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 88 | int(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
|
|
|
Sample Rows
|
|---|
| |
| bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
|---|
| 75 | 240995 | 1286 | 52311 | 0 | 31 | 59852 | 57 | 47868 | + | chr1_KI270762v1_alt | 354444 | 0 | 354444 | chr1 | 248956422 | 2448810 | 2791270 | 88 | 181010,4993,16,8418,4353,1806,28,41,78,41,40,40,42,9,30,78,82,40,41,37,38,46,117,42,77,9,79,72,22,7,22,28,103,21,39,41,37,5,113, ... | 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, ... |
| 85 | 130938 | 340 | 147208 | 0 | 27 | 173 | 19 | 29933 | + | chr1_KQ983255v1_alt | 278659 | 0 | 278659 | chr1 | 248956422 | 13004384 | 13312803 | 47 | 175567,850,846,75,862,516,7758,76,92,31,649,798,302,6,339,1507,1609,77,208,325,989,4,182,344,160,433,624,700,173,168,1291,514,24 ... | 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 ... |
| 85 | 109697 | 558 | 125212 | 0 | 34 | 172 | 20 | 2224 | + | chr1_KI270766v1_alt | 256271 | 20632 | 256271 | chr1 | 248956422 | 13075112 | 13312803 | 55 | 1058,336,4501,4740,3509,2328,5057,2048,698,2068,2,5077,12667,10893,5065,2327,8225,4516,2017,2115,1366,4165,2389,4163,398,1384,12 ... | 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 ... |
| 95 | 161108 | 21 | 181331 | 0 | 5 | 7478 | 5 | 14 | + | chr1_KQ458383v1_alt | 349938 | 0 | 349938 | chr1 | 248956422 | 23237485 | 23579959 | 11 | 12870,5676,716,2482,329,8299,1483,1581,2549,3851,302624, | 0,12871,18547,19263,21746,22075,30374,31857,33440,35990,47314, | 23237485,23250355,23256034,23256758,23259240,23259570,23267870,23269354,23270935,23273484,23277335, |
| 12 | 52503 | 73 | 107806 | 0 | 12 | 5754 | 8 | 25 | + | chr1_KZ208904v1_alt | 166136 | 0 | 166136 | chr1 | 248956422 | 28206356 | 28366763 | 21 | 130836,957,13821,280,1272,168,1032,686,1790,808,1063,1544,445,1711,105,900,166,468,458,1603,269, | 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 ... |
| 12 | 45586 | 106 | 58591 | 0 | 6 | 5245 | 13 | 128 | + | chr1_KI270760v1_alt | 109528 | 0 | 109528 | chr1 | 248956422 | 30352190 | 30456601 | 18 | 23343,5,4,88,54,59,1204,553,15703,288,67,8215,125,919,149,2621,253,50633, | 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 ... |
| 17 | 49582 | 16 | 81789 | 0 | 3 | 8968 | 5 | 10 | + | chr1_KZ208905v1_alt | 140355 | 0 | 140355 | chr1 | 248956422 | 72287733 | 72419130 | 9 | 41617,1408,3913,2559,384,2192,2892,1877,74545, | 0,41617,43028,46941,49508,49892,61041,63933,65810, | 72287733,72329353,72330761,72334676,72337235,72337620,72339812,72342705,72344585, |
| 172 | 55295 | 46 | 80388 | 0 | 4 | 5290 | 3 | 12 | + | chr1_KQ458382v1_alt | 141019 | 0 | 141019 | chr1 | 248956422 | 103909380 | 104045121 | 8 | 4043,17310,696,6179,617,2062,1744,103078, | 0,4043,21353,22051,28238,34134,36196,37941, | 103909380,103913427,103930739,103931435,103937614,103938231,103940299,103942043, |
| 21 | 123891 | 331 | 177652 | 0 | 36 | 249146 | 31 | 249726 | + | chr1_KV880763v1_alt | 551020 | 0 | 551020 | chr1 | 248956422 | 107987824 | 108539424 | 66 | 126194,711,551,1226,4877,1642,186,3848,1430,10021,2273,10150,3103,147,411,1319,2749,759,3713,1600,642,5,1650,11087,2455,1,525,13 ... | 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 ... |
| 176 | 92811 | 561 | 155334 | 0 | 49 | 102 | 52 | 435 | - | chr1_KV880763v1_alt | 551020 | 234766 | 483574 | chr1 | 248956422 | 108222601 | 108471742 | 102 | 54,42,46,1757,3759,6608,196,9878,1013,518,1144,192,146,4707,1389,1753,690,1231,775,7506,104,6680,943,3588,2474,294,35,14055,9272 ... | 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.
| |
|
|
|
US Server