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Database: ce2 Primary Table: xenoRefSeqAli Row Count: 33,808   Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 317 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 165 | 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 | 6 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 409 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 6 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 2695 | 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_205425 | varchar(255) | values | Query sequence name |
qSize | 1353 | int(10) unsigned | range | Query sequence size |
qStart | 279 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1170 | int(10) unsigned | range | Alignment end position in query |
tName | chrI | varchar(255) | values | Target sequence name |
tSize | 15080483 | int(10) unsigned | range | Target sequence size |
tStart | 74622 | int(10) unsigned | range | Alignment start position in target |
tEnd | 77799 | int(10) unsigned | range | Alignment end position in target |
blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 114,39,14,54,135,42,84, | longblob | | Size of each block |
qStarts | 279,462,612,795,888,1035,1086, | longblob | | Start of each block in query. |
tStarts | 74622,75170,75374,76020,769... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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ce2.all_est.qName (via xenoRefSeqAli.qName)
ce2.all_mrna.qName (via xenoRefSeqAli.qName)
ce2.refGene.name (via xenoRefSeqAli.qName)
ce2.refSeqAli.qName (via xenoRefSeqAli.qName)
ce2.xenoRefFlat.name (via xenoRefSeqAli.qName)
ce2.xenoRefGene.name (via xenoRefSeqAli.qName)
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)
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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 | 317 | 165 | 0 | 0 | 6 | 409 | 6 | 2695 | ++ | NM_205425 | 1353 | 279 | 1170 | chrI | 15080483 | 74622 | 77799 | 7 | 114,39,14,54,135,42,84, | 279,462,612,795,888,1035,1086, | 74622,75170,75374,76020,76949,77105,77715, |
593 | 517 | 305 | 0 | 0 | 3 | 168 | 9 | 8692 | +- | NM_007279 | 2146 | 502 | 1492 | chrIII | 13783313 | 1063008 | 1072522 | 10 | 144,3,123,75,60,57,60,171,3,126, | 502,646,649,817,892,958,1015,1192,1363,1366, | 12710791,12711077,12712669,12712828,12715373,12715436,12718363,12718513,12718734,12720179, |
656 | 225 | 99 | 0 | 0 | 0 | 0 | 1 | 45 | ++ | NM_001360932 | 979 | 310 | 634 | chrIII | 13783313 | 9331720 | 9332089 | 2 | 160,164, | 310,470, | 9331720,9331925, |
741 | 411 | 216 | 0 | 0 | 1 | 123 | 2 | 405 | ++ | NM_001325974 | 917 | 1 | 751 | chrV | 20922231 | 20477739 | 20478771 | 3 | 204,70,353, | 1,328,398, | 20477739,20478292,20478418, |
596 | 602 | 331 | 0 | 0 | 5 | 585 | 4 | 1129 | ++ | NM_001324682 | 2079 | 370 | 1888 | chrX | 17718849 | 1481978 | 1484040 | 6 | 57,90,30,303,195,258, | 370,481,572,604,1282,1630, | 1481978,1482148,1482238,1482271,1482995,1483782, |
585 | 321 | 168 | 0 | 0 | 1 | 15 | 2 | 111 | +- | NM_001029971 | 1317 | 170 | 674 | chrI | 15080483 | 109357 | 109957 | 3 | 114,279,96, | 170,299,578, | 14970526,14970706,14971030, |
648 | 467 | 235 | 0 | 0 | 2 | 24 | 3 | 159 | ++ | NM_001325274 | 1519 | 302 | 1028 | chrIV | 17493791 | 8361862 | 8362723 | 4 | 60,234,294,114, | 302,377,611,914, | 8361862,8361934,8362253,8362609, |
585 | 326 | 157 | 0 | 0 | 1 | 21 | 2 | 117 | +- | NM_001146600 | 1368 | 264 | 768 | chrI | 15080483 | 109357 | 109957 | 3 | 120,267,96, | 264,405,672, | 14970526,14970718,14971030, |
611 | 764 | 313 | 0 | 0 | 3 | 264 | 5 | 1922 | ++ | NM_006796 | 3160 | 784 | 2125 | chrI | 15080483 | 3469554 | 3472553 | 6 | 39,342,81,132,372,111, | 784,1051,1393,1495,1642,2014, | 3469554,3470763,3471108,3471213,3471354,3472442, |
676 | 361 | 173 | 0 | 0 | 2 | 195 | 4 | 1330 | +- | NM_000365 | 1351 | 48 | 777 | chrII | 15279308 | 12037162 | 12039026 | 5 | 39,139,2,96,258, | 48,219,358,360,519, | 3240282,3240453,3240781,3240817,3241888, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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