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Database: mm10 Primary Table: xenoRefSeqAli Row Count: 193,238   Data last updated: 2020-08-17
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 1076 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 748 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 214 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 0 | 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 | 10 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 1295 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 11 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 1628 | int(10) unsigned | range | Number of bases inserted in target |
strand | +- | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | NM_032135 | varchar(255) | values | Query sequence name |
qSize | 3135 | int(10) unsigned | range | Query sequence size |
qStart | 270 | int(10) unsigned | range | Alignment start position in query |
qEnd | 2527 | int(10) unsigned | range | Alignment end position in query |
tName | chr12 | varchar(255) | values | Target sequence name |
tSize | 120129022 | int(10) unsigned | range | Target sequence size |
tStart | 64472045 | int(10) unsigned | range | Alignment start position in target |
tEnd | 64474635 | int(10) unsigned | range | Alignment end position in target |
blockCount | 12 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 57,183,153,57,10,27,87,54,2... | longblob | | Size of each block |
qStarts | 270,368,680,1167,1255,1286,... | longblob | | Start of each block in query. |
tStarts | 55654387,55654485,55654794,... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
mm10.all_est.qName (via xenoRefSeqAli.qName)
mm10.all_mrna.qName (via xenoRefSeqAli.qName)
mm10.refGene.name (via xenoRefSeqAli.qName)
mm10.refSeqAli.qName (via xenoRefSeqAli.qName)
mm10.xenoMrna.qName (via xenoRefSeqAli.qName)
mm10.xenoRefFlat.name (via xenoRefSeqAli.qName)
mm10.xenoRefGene.name (via xenoRefSeqAli.qName)
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Sample Rows
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bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
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1076 | 748 | 214 | 0 | 0 | 10 | 1295 | 11 | 1628 | +- | NM_032135 | 3135 | 270 | 2527 | chr12 | 120129022 | 64472045 | 64474635 | 12 | 57,183,153,57,10,27,87,54,24,139,126,45, | 270,368,680,1167,1255,1286,1341,1800,1949,2105,2244,2482, | 55654387,55654485,55654794,55655143,55655462,55655661,55655716,55655860,55655928,55655967,55656394,55656932, |
76 | 3118 | 243 | 0 | 0 | 14 | 336 | 14 | 454573 | +- | NM_001011971 | 3727 | 14 | 3711 | chr1 | 195471971 | 3214479 | 3672413 | 21 | 186,17,54,129,58,76,416,200,1046,82,82,63,24,118,34,45,97,52,123,262,197, | 14,200,220,280,410,468,544,960,1160,2217,2316,2401,2479,2740,2871,2905,2951,3054,3108,3248,3514, | 191799558,191799745,191799762,191799823,191799952,191800015,191801004,192050070,192255003,192256049,192256133,192256217,19225629 ... |
76 | 1770 | 171 | 0 | 0 | 3 | 147 | 3 | 453512 | +- | NM_001033036 | 2343 | 60 | 2148 | chr1 | 195471971 | 3215935 | 3671388 | 6 | 179,267,262,200,961,72, | 60,374,644,906,1106,2076, | 191800583,191800891,191801158,192050070,192255003,192255964, |
76 | 1197 | 370 | 0 | 0 | 6 | 345 | 9 | 453816 | +- | NM_001012258 | 2209 | 58 | 1970 | chr1 | 195471971 | 3215965 | 3671348 | 10 | 39,69,244,45,15,88,195,569,282,21, | 58,97,241,571,627,661,749,944,1615,1949, | 191800623,191800665,191800905,191801238,191801303,191801337,192050075,192255003,192255668,192255985, |
76 | 1386 | 324 | 0 | 0 | 2 | 147 | 6 | 453620 | +- | NM_001032307 | 2993 | 112 | 1969 | chr1 | 195471971 | 3216021 | 3671351 | 7 | 41,85,255,59,123,200,947, | 112,153,344,640,699,822,1022, | 191800620,191800664,191800894,191801214,191801297,192050070,192255003, |
76 | 862 | 299 | 0 | 0 | 4 | 336 | 7 | 454169 | +- | NM_001032714 | 1804 | 38 | 1535 | chr1 | 195471971 | 3216021 | 3671351 | 8 | 42,69,258,39,77,202,213,261, | 38,80,231,566,656,733,935,1274, | 191800620,191800665,191800900,191801238,191801343,192050070,192255359,192255689, |
613 | 382 | 111 | 0 | 0 | 4 | 191 | 5 | 302 | +- | NM_001077752 | 966 | 84 | 768 | chr1 | 195471971 | 3670553 | 3671348 | 6 | 39,69,244,45,15,81, | 84,123,267,597,653,687, | 191800623,191800665,191800905,191801238,191801303,191801337, |
618 | 5973 | 688 | 0 | 0 | 10 | 319 | 16 | 9578 | +- | NM_001195676 | 6991 | 0 | 6980 | chr1 | 195471971 | 4344153 | 4360392 | 20 | 149,31,647,172,11,214,123,813,1222,477,19,253,927,1067,215,158,27,64,44,28, | 0,149,180,827,999,1010,1224,1355,2168,3390,3886,4049,4305,5247,6314,6613,6775,6836,6906,6952, | 191111579,191111730,191119123,191119890,191121880,191121897,191122114,191122242,191123058,191124283,191124764,191124903,19112515 ... |
618 | 2595 | 644 | 0 | 0 | 22 | 3085 | 21 | 4915 | +- | NM_001003040 | 6834 | 63 | 6387 | chr1 | 195471971 | 4344605 | 4352759 | 26 | 556,174,20,197,104,48,36,61,11,30,36,96,106,479,77,73,187,187,61,530,45,17,5,10,60,33, | 63,619,793,862,1202,1338,1446,1485,1552,1649,1927,2301,2658,3126,4299,4376,4586,4874,5280,5342,6030,6108,6166,6172,6185,6354, | 191119212,191119888,191121880,191121943,191122274,191122404,191122506,191122542,191122603,191122703,191122966,191123337,19112369 ... |
618 | 3401 | 866 | 0 | 0 | 23 | 2132 | 23 | 3953 | +- | NM_001280013 | 6461 | 0 | 6399 | chr1 | 195471971 | 4344605 | 4352825 | 27 | 43,370,179,186,249,105,99,36,66,192,19,29,12,96,54,314,599,20,118,11,72,61,97,315,738,66,121, | 0,46,429,608,850,1191,1329,1437,1476,1560,1859,1930,2010,2244,2428,2527,2998,3928,3955,4160,4297,4369,4568,4665,5148,6186,6278, | 191119146,191119189,191119590,191119889,191121943,191122275,191122407,191122506,191122542,191122617,191122913,191122972,19112304 ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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