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Database: panPan2 Primary Table: ncbiRefSeqPsl Row Count: 59,355   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 | 591 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 2322 | 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 | 28 | 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 | 11 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 17557 | 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_014343994.1 | varchar(255) | values | Query sequence name |
qSize | 2350 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 2350 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 229774977 | int(10) unsigned | range | Target sequence size |
tStart | 823526 | int(10) unsigned | range | Alignment start position in target |
tEnd | 843433 | int(10) unsigned | range | Alignment end position in target |
blockCount | 12 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 291,92,182,51,125,90,138,16... | longblob | | Size of each block |
qStarts | 0,291,383,565,616,741,831,9... | longblob | | Start of each block in query. |
tStarts | 823526,824874,828949,829835... | 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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591 | 2322 | 0 | 28 | 0 | 0 | 0 | 11 | 17557 | + | XM_014343994.1 | 2350 | 0 | 2350 | chr1 | 229774977 | 823526 | 843433 | 12 | 291,92,182,51,125,90,138,163,311,125,111,671, | 0,291,383,565,616,741,831,969,1132,1443,1568,1679, | 823526,824874,828949,829835,833690,836810,837045,839962,841590,842110,842552,842762, |
591 | 2168 | 0 | 70 | 0 | 0 | 0 | 14 | 10655 | - | XM_008961355.1 | 2238 | 0 | 2238 | chr1 | 229774977 | 843061 | 855954 | 15 | 596,105,136,114,102,114,112,140,189,114,111,79,91,121,114, | 0,596,701,837,951,1053,1167,1279,1419,1608,1722,1833,1912,2003,2124, | 843061,843898,844374,845031,846995,847354,850025,850937,851349,852112,852719,852941,854860,855031,855840, |
591 | 2312 | 0 | 70 | 0 | 0 | 0 | 15 | 10511 | - | XM_003804574.2 | 2382 | 0 | 2382 | chr1 | 229774977 | 843061 | 855954 | 16 | 596,105,136,114,144,102,114,112,140,189,114,111,79,91,121,114, | 0,596,701,837,951,1095,1197,1311,1423,1563,1752,1866,1977,2056,2147,2268, | 843061,843898,844374,845031,845260,846995,847354,850025,850937,851349,852112,852719,852941,854860,855031,855840, |
591 | 1503 | 0 | 0 | 0 | 0 | 0 | 9 | 2621 | + | XM_014342495.2 | 1503 | 0 | 1503 | chr1 | 229774977 | 859735 | 863859 | 10 | 211,122,222,117,214,145,168,89,74,141, | 0,211,333,555,672,886,1031,1199,1288,1362, | 859735,860022,860244,860768,861117,861522,861750,862333,862525,863718, |
591 | 2233 | 0 | 51 | 0 | 0 | 0 | 10 | 2452 | + | XR_001337708.1 | 2284 | 0 | 2284 | chr1 | 229774977 | 859735 | 864471 | 11 | 211,122,222,117,214,145,168,89,61,182,753, | 0,211,333,555,672,886,1031,1199,1288,1349,1531, | 859735,860022,860244,860768,861117,861522,861750,862333,862525,862767,863718, |
591 | 2251 | 0 | 51 | 0 | 0 | 0 | 10 | 2439 | + | XM_008961362.1 | 2302 | 0 | 2302 | chr1 | 229774977 | 859735 | 864476 | 11 | 211,122,222,117,214,145,168,89,74,182,758, | 0,211,333,555,672,886,1031,1199,1288,1362,1544, | 859735,860022,860244,860768,861117,861522,861750,862333,862525,862767,863718, |
591 | 3210 | 0 | 276 | 0 | 1 | 1 | 15 | 6403 | + | XM_008961383.3 | 3487 | 0 | 3487 | chr1 | 229774977 | 864965 | 874854 | 17 | 407,100,147,81,73,128,132,81,76,137,150,141,141,198,32,49,1413, | 0,407,507,654,735,808,936,1068,1149,1225,1362,1512,1653,1794,1993,2025,2074, | 864965,865461,868860,869104,869269,869462,869660,869907,870657,870870,871848,872173,872487,872820,873018,873315,873441, |
591 | 2996 | 0 | 178 | 0 | 0 | 0 | 4 | 3625 | - | XM_008961378.1 | 3174 | 0 | 3174 | chr1 | 229774977 | 874194 | 880993 | 5 | 1064,126,1894,37,53, | 0,1064,1190,3084,3121, | 874194,875487,877639,880012,880940, |
591 | 3482 | 0 | 178 | 0 | 0 | 0 | 3 | 3146 | - | XM_008961370.1 | 3660 | 0 | 3660 | chr1 | 229774977 | 874194 | 881000 | 4 | 1064,126,2410,60, | 0,1064,1190,3600, | 874194,875487,877639,880940, |
592 | 668 | 0 | 0 | 0 | 0 | 0 | 1 | 407 | + | XM_003805983.3 | 668 | 0 | 668 | chr1 | 229774977 | 927416 | 928491 | 2 | 111,557, | 0,111, | 927416,927934, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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