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Database: caeJap1 Primary Table: xenoRefSeqAli Row Count: 203,513   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 | info | description |
bin | 1297 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 112 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 38 | 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 | 2 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 1332 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 2 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 2054 | 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_001322547 | varchar(255) | values | Query sequence name |
qSize | 1756 | int(10) unsigned | range | Query sequence size |
qStart | 174 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1656 | int(10) unsigned | range | Alignment end position in query |
tName | chrUn | varchar(255) | values | Target sequence name |
tSize | 156378573 | int(10) unsigned | range | Target sequence size |
tStart | 93402952 | int(10) unsigned | range | Alignment start position in target |
tEnd | 93405156 | int(10) unsigned | range | Alignment end position in target |
blockCount | 3 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 60,45,45, | longblob | | Size of each block |
qStarts | 174,649,1611, | longblob | | Start of each block in query. |
tStarts | 93402952,93403627,93405111, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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caeJap1.all_est.qName (via xenoRefSeqAli.qName)
caeJap1.all_mrna.qName (via xenoRefSeqAli.qName)
caeJap1.xenoMrna.qName (via xenoRefSeqAli.qName)
caeJap1.xenoRefFlat.name (via xenoRefSeqAli.qName)
caeJap1.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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1297 | 112 | 38 | 0 | 0 | 2 | 1332 | 2 | 2054 | ++ | NM_001322547 | 1756 | 174 | 1656 | chrUn | 156378573 | 93402952 | 93405156 | 3 | 60,45,45, | 174,649,1611, | 93402952,93403627,93405111, |
1297 | 112 | 38 | 0 | 0 | 2 | 1332 | 2 | 2054 | ++ | NM_001322548 | 1644 | 87 | 1569 | chrUn | 156378573 | 93402952 | 93405156 | 3 | 60,45,45, | 87,562,1524, | 93402952,93403627,93405111, |
1297 | 413 | 113 | 0 | 17 | 2 | 72 | 3 | 1273 | +- | NM_077642 | 1046 | 7 | 622 | chrUn | 156378573 | 93429205 | 93431021 | 4 | 45,114,165,219, | 7,109,238,403, | 62947552,62947966,62948142,62949149, |
1101 | 748 | 234 | 0 | 0 | 2 | 17 | 2 | 3072 | ++ | NM_072248 | 1177 | 73 | 1072 | chrUn | 156378573 | 67716636 | 67720690 | 3 | 93,546,343, | 73,181,729, | 67716636,67716802,67720347, |
1300 | 539 | 260 | 0 | 20 | 1 | 3 | 5 | 200 | ++ | NM_065073 | 1155 | 270 | 1092 | chrUn | 156378573 | 93746860 | 93747879 | 6 | 46,175,181,3,285,129, | 270,316,491,672,675,963, | 93746860,93746951,93747170,93747383,93747411,93747750, |
954 | 607 | 252 | 0 | 71 | 0 | 0 | 5 | 1105 | +- | NM_063298 | 1148 | 25 | 955 | chrUn | 156378573 | 48390348 | 48392383 | 6 | 237,137,144,3,159,250, | 25,262,399,543,546,705, | 107986190,107986475,107986659,107986848,107987768,107987975, |
751 | 235 | 104 | 0 | 0 | 2 | 201 | 2 | 262 | +- | NM_001306614 | 798 | 147 | 687 | chrUn | 156378573 | 21883538 | 21884139 | 3 | 105,126,108, | 147,429,579, | 134494434,134494777,134494927, |
736 | 79 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_070297 | 86 | 3 | 86 | chrUn | 156378573 | 19916583 | 19916666 | 1 | 83, | 3, | 136461907, |
585 | 738 | 452 | 0 | 19 | 4 | 60 | 7 | 314 | +- | NM_001006831 | 2353 | 587 | 1856 | chrUn | 156378573 | 39720 | 41243 | 8 | 226,146,75,537,54,63,3,105, | 587,813,971,1052,1619,1685,1748,1751, | 156337330,156337606,156337764,156337897,156338521,156338635,156338728,156338748, |
585 | 748 | 442 | 0 | 19 | 4 | 60 | 7 | 314 | +- | NM_001092595 | 2544 | 580 | 1849 | chrUn | 156378573 | 39720 | 41243 | 8 | 226,146,75,537,54,63,3,105, | 580,806,964,1045,1612,1678,1741,1744, | 156337330,156337606,156337764,156337897,156338521,156338635,156338728,156338748, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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