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Database: chrPic1 Primary Table: xenoRefSeqAli Row Count: 525,053   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 615 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 64 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 21 | 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 | 0 | int(10) unsigned | Number of inserts in query |
qBaseInsert | 0 | int(10) unsigned | Number of bases inserted in query |
tNumInsert | 0 | int(10) unsigned | Number of inserts in target |
tBaseInsert | 0 | int(10) unsigned | Number of bases inserted in target |
strand | +- | char(2) | + or - for strand. First character query, second target (optional) |
qName | NM_176882 | varchar(255) | Query sequence name |
qSize | 1043 | int(10) unsigned | Query sequence size |
qStart | 366 | int(10) unsigned | Alignment start position in query |
qEnd | 451 | int(10) unsigned | Alignment end position in query |
tName | JH584713 | varchar(255) | Target sequence name |
tSize | 6329327 | int(10) unsigned | Target sequence size |
tStart | 3998594 | int(10) unsigned | Alignment start position in target |
tEnd | 3998679 | int(10) unsigned | Alignment end position in target |
blockCount | 1 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 85, | longblob | Size of each block |
qStarts | 366, | longblob | Start of each block in query. |
tStarts | 2330648, | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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chrPic1.all_mrna.qName (via xenoRefSeqAli.qName)
chrPic1.xenoMrna.qName (via xenoRefSeqAli.qName)
chrPic1.xenoRefFlat.name (via xenoRefSeqAli.qName)
chrPic1.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 |
---|
615 | 64 | 21 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_176882 | 1043 | 366 | 451 | JH584713 | 6329327 | 3998594 | 3998679 | 1 | 85, | 366, | 2330648, |
76 | 682 | 244 | 0 | 22 | 5 | 1263 | 7 | 102925 | ++ | NM_001353686 | 7236 | 2076 | 4287 | JH584725 | 5579271 | 3206368 | 3310241 | 8 | 93,3,213,189,69,108,177,96, | 2076,2169,2172,2394,3681,3870,3984,4191, | 3206368,3207279,3209228,3222952,3302516,3305502,3306330,3310145, |
586 | 175 | 100 | 0 | 19 | 2 | 2692 | 2 | 45175 | +- | NM_003386 | 8700 | 5143 | 8129 | JH584416 | 3140404 | 211063 | 256532 | 3 | 96,99,99, | 5143,6391,8030, | 2883872,2902704,2929242, |
585 | 102 | 33 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001127976 | 3267 | 1354 | 1489 | AHGY01246055 | 1980 | 1045 | 1180 | 1 | 135, | 1354, | 1045, |
585 | 313 | 91 | 0 | 7 | 0 | 0 | 1 | 394 | ++ | NM_001101275 | 1102 | 242 | 653 | AHGY01246363 | 1966 | 930 | 1735 | 2 | 252,159, | 242,494, | 930,1576, |
585 | 206 | 58 | 0 | 0 | 0 | 0 | 1 | 394 | ++ | NM_010584 | 1149 | 235 | 499 | AHGY01246363 | 1966 | 932 | 1590 | 2 | 250,14, | 235,485, | 932,1576, |
585 | 210 | 57 | 0 | 0 | 0 | 0 | 1 | 394 | ++ | NM_001007552 | 1136 | 225 | 492 | AHGY01246363 | 1966 | 932 | 1593 | 2 | 250,17, | 225,475, | 932,1576, |
585 | 211 | 56 | 0 | 0 | 0 | 0 | 1 | 394 | ++ | NM_001034946 | 1143 | 223 | 490 | AHGY01246363 | 1966 | 932 | 1593 | 2 | 250,17, | 223,473, | 932,1576, |
585 | 260 | 126 | 0 | 7 | 0 | 0 | 1 | 394 | ++ | NM_001159584 | 1297 | 368 | 761 | AHGY01246363 | 1966 | 933 | 1720 | 2 | 249,144, | 368,617, | 933,1576, |
585 | 283 | 115 | 0 | 7 | 0 | 0 | 1 | 394 | ++ | NM_001088042 | 1081 | 183 | 588 | AHGY01246363 | 1966 | 933 | 1732 | 2 | 249,156, | 183,432, | 933,1576, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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