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Database: geoFor1 Primary Table: xenoRefSeqAli Row Count: 378,647   Data last updated: 2020-08-19
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 | 250 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 103 | 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 | 19 | int(10) unsigned | range | Number of 'N' bases |
qNumInsert | 2 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 144 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 2 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 10047 | 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_001001290 | varchar(255) | values | Query sequence name |
qSize | 1885 | int(10) unsigned | range | Query sequence size |
qStart | 225 | int(10) unsigned | range | Alignment start position in query |
qEnd | 741 | int(10) unsigned | range | Alignment end position in query |
tName | JH739887 | varchar(255) | values | Target sequence name |
tSize | 30495534 | int(10) unsigned | range | Target sequence size |
tStart | 9140 | int(10) unsigned | range | Alignment start position in target |
tEnd | 19559 | int(10) unsigned | range | Alignment end position in target |
blockCount | 3 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 90,156,126, | longblob | | Size of each block |
qStarts | 225,327,615, | longblob | | Start of each block in query. |
tStarts | 30475975,30480936,30486268, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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geoFor1.all_mrna.qName (via xenoRefSeqAli.qName)
geoFor1.xenoRefFlat.name (via xenoRefSeqAli.qName)
geoFor1.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 |
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585 | 250 | 103 | 0 | 19 | 2 | 144 | 2 | 10047 | +- | NM_001001290 | 1885 | 225 | 741 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,126, | 225,327,615, | 30475975,30480936,30486268, |
585 | 247 | 115 | 0 | 19 | 2 | 135 | 2 | 10038 | +- | NM_001012363 | 3403 | 72 | 588 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,135, | 72,174,453, | 30475975,30480936,30486259, |
585 | 247 | 115 | 0 | 19 | 2 | 135 | 2 | 10038 | +- | NM_001102414 | 3602 | 271 | 787 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,135, | 271,373,652, | 30475975,30480936,30486259, |
585 | 247 | 115 | 0 | 19 | 2 | 135 | 2 | 10038 | +- | NM_001102415 | 3281 | 271 | 787 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,135, | 271,373,652, | 30475975,30480936,30486259, |
585 | 235 | 88 | 0 | 19 | 2 | 174 | 2 | 10077 | +- | NM_001130835 | 1761 | 140 | 656 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,117,135, | 140,242,521, | 30475975,30480936,30486259, |
585 | 250 | 112 | 0 | 19 | 2 | 135 | 2 | 10038 | +- | NM_001191551 | 3384 | 117 | 633 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,135, | 117,219,498, | 30475975,30480936,30486259, |
632 | 663 | 175 | 0 | 38 | 1 | 111 | 6 | 2915 | ++ | NM_000925 | 1507 | 116 | 1103 | JH739907 | 8707472 | 6192607 | 6196398 | 7 | 114,60,36,285,97,140,144, | 116,230,290,326,722,819,959, | 6192607,6192792,6192935,6193057,6194784,6195815,6196254, |
585 | 247 | 115 | 0 | 19 | 2 | 135 | 2 | 10038 | +- | NM_145559 | 3276 | 266 | 782 | JH739887 | 30495534 | 9140 | 19559 | 3 | 90,156,135, | 266,368,647, | 30475975,30480936,30486259, |
585 | 62 | 31 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001140649 | 848 | 366 | 459 | JH739887 | 30495534 | 14442 | 14535 | 1 | 93, | 366, | 30480999, |
585 | 78 | 39 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001020494 | 1950 | 262 | 379 | JH739887 | 30495534 | 14481 | 14598 | 1 | 117, | 262, | 30480936, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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