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Database: xenTro1 Primary Table: xenoRefSeqAli Row Count: 582,134   Data last updated: 2020-09-02
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 2041 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 152 | int(10) unsigned | Number of bases that don't match |
repMatches | 0 | int(10) unsigned | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | Number of 'N' bases |
qNumInsert | 15 | int(10) unsigned | Number of inserts in query |
qBaseInsert | 853 | int(10) unsigned | Number of bases inserted in query |
tNumInsert | 22 | int(10) unsigned | Number of inserts in target |
tBaseInsert | 17696 | int(10) unsigned | Number of bases inserted in target |
strand | +- | char(2) | + or - for strand. First character query, second target (optional) |
qName | NM_001096477 | varchar(255) | Query sequence name |
qSize | 3091 | int(10) unsigned | Query sequence size |
qStart | 0 | int(10) unsigned | Alignment start position in query |
qEnd | 3046 | int(10) unsigned | Alignment end position in query |
tName | scaffold_1 | varchar(255) | Target sequence name |
tSize | 7608560 | int(10) unsigned | Target sequence size |
tStart | 3642 | int(10) unsigned | Alignment start position in target |
tEnd | 23531 | int(10) unsigned | Alignment end position in target |
blockCount | 28 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 100,61,166,134,110,93,50,12... | longblob | Size of each block |
qStarts | 0,100,162,328,462,572,665,7... | longblob | Start of each block in query. |
tStarts | 7585029,7585132,7585193,759... | 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)
xenTro1.all_est.qName (via xenoRefSeqAli.qName)
xenTro1.all_mrna.qName (via xenoRefSeqAli.qName)
xenTro1.xenoRefFlat.name (via xenoRefSeqAli.qName)
xenTro1.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 |
---|
585 | 2041 | 152 | 0 | 0 | 15 | 853 | 22 | 17696 | +- | NM_001096477 | 3091 | 0 | 3046 | scaffold_1 | 7608560 | 3642 | 23531 | 28 | 100,61,166,134,110,93,50,128,85,132,90,104,96,85,192,21,10,61,90,7,14,25,95,22,12,105,34,71, | 0,100,162,328,462,572,665,715,843,928,1060,1150,1385,1482,1570,1763,1788,1799,1876,1967,1974,1988,2024,2176,2217,2833,2940,2975, | 7585029,7585132,7585193,7590056,7595413,7597917,7598409,7598922,7600450,7601753,7602116,7602770,7603817,7603920,7604005,7604197, ... |
585 | 954 | 260 | 0 | 0 | 4 | 1199 | 13 | 18440 | +- | NM_001035255 | 2654 | 175 | 2588 | scaffold_1 | 7608560 | 3657 | 23311 | 14 | 109,1,134,105,94,55,132,60,131,97,90,66,57,83, | 175,284,285,419,524,618,673,823,883,1014,1111,1339,1480,2505, | 7585249,7585377,7590056,7595413,7597912,7598405,7598923,7600476,7601754,7602116,7602777,7603817,7603958,7604820, |
585 | 970 | 239 | 0 | 0 | 4 | 1306 | 12 | 18445 | +- | NM_001044587 | 2787 | 204 | 2719 | scaffold_1 | 7608560 | 3657 | 23311 | 13 | 107,137,105,94,54,133,60,131,97,90,66,69,66, | 204,311,448,553,647,701,852,912,1043,1140,1368,1497,2653, | 7585249,7590053,7595413,7597912,7598405,7598922,7600476,7601754,7602116,7602777,7603817,7603943,7604837, |
592 | 836 | 328 | 0 | 0 | 6 | 642 | 11 | 39588 | +- | NM_030721 | 3982 | 509 | 2315 | scaffold_158 | 1964590 | 973400 | 1014152 | 12 | 54,69,141,90,174,87,119,2,104,114,90,120, | 509,665,758,899,1094,1268,1391,1510,1512,1754,2105,2195, | 950438,951875,953237,954955,964136,965471,968510,968669,969732,983425,988909,991070, |
592 | 836 | 328 | 0 | 0 | 6 | 642 | 11 | 39588 | +- | NM_001357019 | 3978 | 505 | 2311 | scaffold_158 | 1964590 | 973400 | 1014152 | 12 | 54,69,141,90,174,87,119,2,104,114,90,120, | 505,661,754,895,1090,1264,1387,1506,1508,1750,2101,2191, | 950438,951875,953237,954955,964136,965471,968510,968669,969732,983425,988909,991070, |
592 | 1814 | 356 | 0 | 0 | 26 | 1671 | 33 | 47437 | +- | NM_001364637 | 3861 | 16 | 3857 | scaffold_199 | 1794310 | 961541 | 1011148 | 39 | 138,148,162,78,540,462,12,7,69,36,11,39,6,18,15,15,18,18,8,11,31,14,10,12,31,15,43,41,14,13,13,7,25,21,5,11,10,12,31, | 16,299,548,710,788,1328,1846,1859,1883,2045,2197,2288,2327,2333,2360,2570,2589,2614,2632,2641,2659,2725,2741,3095,3147,3178,3193 ... | 783162,785141,823533,824547,828667,829210,829753,829767,829855,830067,830329,830463,830505,830512,830546,831194,831212,831238,83 ... |
73 | 636 | 355 | 0 | 0 | 2 | 35 | 8 | 825154 | +- | NR_138063 | 4615 | 1011 | 2037 | scaffold_450 | 1066630 | 141119 | 967264 | 9 | 159,69,22,128,132,51,228,48,154, | 1011,1170,1263,1285,1413,1545,1596,1835,1883, | 99366,110466,110559,135931,306061,350632,805816,860616,925357, |
585 | 984 | 239 | 0 | 0 | 7 | 1286 | 13 | 18432 | +- | NM_001031296 | 2625 | 46 | 2555 | scaffold_1 | 7608560 | 3662 | 23317 | 15 | 114,134,110,89,54,133,60,132,96,90,63,66,15,4,63, | 46,162,296,406,495,549,700,760,892,988,1216,1345,2016,2032,2492, | 7585243,7590056,7595413,7597917,7598405,7598922,7600476,7601754,7602117,7602777,7603820,7603946,7604498,7604513,7604835, |
585 | 908 | 235 | 0 | 0 | 3 | 216 | 12 | 17620 | +- | NM_001075621 | 2432 | 132 | 1491 | scaffold_1 | 7608560 | 4548 | 23311 | 13 | 109,1,134,105,98,51,132,60,131,97,90,66,69, | 132,241,242,376,481,579,630,780,840,971,1068,1296,1422, | 7585249,7585377,7590056,7595413,7597912,7598409,7598923,7600476,7601754,7602116,7602777,7603817,7603943, |
585 | 561 | 217 | 0 | 0 | 5 | 458 | 7 | 17850 | +- | NM_199576 | 2126 | 146 | 1382 | scaffold_1 | 7608560 | 4689 | 23317 | 8 | 114,123,112,99,111,75,93,51, | 146,262,385,680,863,992,1067,1331, | 7585243,7590056,7595402,7598953,7601760,7602132,7602774,7603820, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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