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Database: xenLae2 Primary Table: ncbiRefSeqPsl Row Count: 61,188   Data last updated: 2020-04-01
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 706 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 0 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 192 | 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 | 0 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 0 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 2 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 1356 | int(10) unsigned | range | Number of bases inserted in target |
strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | XM_018226952.1 | varchar(255) | values | Query sequence name |
qSize | 898 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 898 | int(10) unsigned | range | Alignment end position in query |
tName | chr1L | varchar(255) | values | Target sequence name |
tSize | 219802468 | int(10) unsigned | range | Target sequence size |
tStart | 260620 | int(10) unsigned | range | Alignment start position in target |
tEnd | 262874 | int(10) unsigned | range | Alignment end position in target |
blockCount | 3 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 63,208,627, | longblob | | Size of each block |
qStarts | 0,63,271, | longblob | | Start of each block in query. |
tStarts | 260620,261723,262247, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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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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73 | 706 | 0 | 192 | 0 | 0 | 0 | 2 | 1356 | + | XM_018226952.1 | 898 | 0 | 898 | chr1L | 219802468 | 260620 | 262874 | 3 | 63,208,627, | 0,63,271, | 260620,261723,262247, |
588 | 147 | 0 | 34 | 0 | 0 | 0 | 1 | 106 | + | XR_001932207.1 | 181 | 0 | 181 | chr1L | 219802468 | 425661 | 425948 | 2 | 42,139, | 0,42, | 425661,425809, |
589 | 1161 | 6 | 11 | 0 | 2 | 51 | 10 | 38737 | + | NM_001094629.1 | 1273 | 2 | 1231 | chr1L | 219802468 | 532209 | 572124 | 11 | 63,72,31,117,213,8,1,82,152,189,250, | 2,65,137,168,285,513,521,558,640,792,981, | 532209,542406,542479,547429,549061,554813,554822,564262,566076,568062,571874, |
9 | 3653 | 10 | 246 | 0 | 3 | 132 | 19 | 1039641 | - | NM_001092812.1 | 4073 | 0 | 4041 | chr1L | 219802468 | 1289838 | 2333388 | 22 | 176,142,16,805,147,135,106,182,152,201,157,93,153,81,36,204,267,120,167,196,106,267, | 32,223,368,384,1189,1336,1471,1577,1873,2025,2226,2383,2476,2629,2710,2746,2950,3217,3337,3504,3700,3806, | 1289838,1290014,1290156,1290204,1341711,1356137,1378905,1383491,1405914,1409696,1414905,1415690,1547305,1593459,1825156,2103675, ... |
598 | 2682 | 0 | 220 | 0 | 0 | 0 | 0 | 0 | + | XM_018226969.1 | 2902 | 0 | 2902 | chr1L | 219802468 | 1709788 | 1712690 | 1 | 2902, | 0, | 1709788, |
75 | 3534 | 0 | 368 | 0 | 0 | 0 | 1 | 73516 | + | XM_018226972.1 | 3902 | 0 | 3902 | chr1L | 219802468 | 2734688 | 2812106 | 2 | 1926,1976, | 0,1926, | 2734688,2810130, |
606 | 1087 | 0 | 48 | 0 | 0 | 0 | 0 | 0 | - | XM_018268147.1 | 1135 | 0 | 1135 | chr1L | 219802468 | 2828932 | 2830067 | 1 | 1135, | 0, | 2828932, |
606 | 716 | 0 | 188 | 0 | 0 | 0 | 0 | 0 | + | XM_018226974.1 | 904 | 0 | 904 | chr1L | 219802468 | 2845147 | 2846051 | 1 | 904, | 0, | 2845147, |
607 | 1714 | 0 | 161 | 0 | 0 | 0 | 5 | 12061 | - | XM_018226987.1 | 1875 | 0 | 1875 | chr1L | 219802468 | 2895508 | 2909444 | 6 | 434,697,174,227,236,107, | 0,434,1131,1305,1532,1768, | 2895508,2899561,2901295,2902628,2903480,2909337, |
607 | 1875 | 0 | 161 | 0 | 0 | 0 | 6 | 11900 | - | XM_018226982.1 | 2036 | 0 | 2036 | chr1L | 219802468 | 2895508 | 2909444 | 7 | 434,161,697,174,227,236,107, | 0,434,595,1292,1466,1693,1929, | 2895508,2896589,2899561,2901295,2902628,2903480,2909337, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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