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Database: turTru2 Primary Table: xenoRefSeqAli Row Count: 583,163   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 73 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 1518 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 281 | 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 | 13 | int(10) unsigned | Number of inserts in query |
qBaseInsert | 2140 | int(10) unsigned | Number of bases inserted in query |
tNumInsert | 15 | int(10) unsigned | Number of inserts in target |
tBaseInsert | 114008 | int(10) unsigned | Number of bases inserted in target |
strand | ++ | char(2) | + or - for strand. First character query, second target (optional) |
qName | NM_001199540 | varchar(255) | Query sequence name |
qSize | 6786 | int(10) unsigned | Query sequence size |
qStart | 2847 | int(10) unsigned | Alignment start position in query |
qEnd | 6786 | int(10) unsigned | Alignment end position in query |
tName | JH473069 | varchar(255) | Target sequence name |
tSize | 329601 | int(10) unsigned | Target sequence size |
tStart | 54224 | int(10) unsigned | Alignment start position in target |
tEnd | 170031 | int(10) unsigned | Alignment end position in target |
blockCount | 19 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 184,37,81,35,61,23,112,148,... | longblob | Size of each block |
qStarts | 2847,3031,3090,3174,3209,32... | longblob | Start of each block in query. |
tStarts | 54224,56284,56322,56403,612... | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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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)
turTru2.xenoRefFlat.name (via xenoRefSeqAli.qName)
turTru2.xenoRefGene.name (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 |
---|
73 | 1518 | 281 | 0 | 0 | 13 | 2140 | 15 | 114008 | ++ | NM_001199540 | 6786 | 2847 | 6786 | JH473069 | 329601 | 54224 | 170031 | 19 | 184,37,81,35,61,23,112,148,246,108,45,18,41,52,47,97,50,88,326, | 2847,3031,3090,3174,3209,3291,3338,3450,3741,4428,4753,4831,4852,4893,4945,4997,5166,6327,6460, | 54224,56284,56322,56403,61253,61314,61337,61897,167217,167754,168051,168119,168156,168209,168263,168316,168481,169572,169705, |
585 | 111 | 14 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001145937 | 10958 | 2632 | 2757 | ABRN02000283 | 639 | 411 | 536 | 1 | 125, | 2632, | 411, |
585 | 111 | 14 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_011857 | 10978 | 2659 | 2784 | ABRN02000283 | 639 | 411 | 536 | 1 | 125, | 2659, | 411, |
585 | 57 | 27 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_076852 | 2699 | 2253 | 2337 | JH481854 | 69204 | 12810 | 12894 | 1 | 84, | 2253, | 56310, |
585 | 98 | 7 | 0 | 30 | 1 | 6 | 0 | 0 | ++ | NM_001163935 | 2597 | 1 | 142 | ABRN02000351 | 228 | 10 | 145 | 2 | 104,31, | 1,111, | 10,114, |
585 | 213 | 102 | 0 | 0 | 3 | 1473 | 3 | 33516 | +- | NM_001018230 | 4139 | 1819 | 3607 | JH477135 | 105512 | 54245 | 88076 | 4 | 108,99,60,48, | 1819,1984,2146,3559, | 17436,18897,20165,51219, |
585 | 157 | 86 | 0 | 0 | 2 | 342 | 2 | 165 | +- | NM_079819 | 1542 | 411 | 996 | JH473910 | 229819 | 74417 | 74825 | 3 | 81,141,21, | 411,588,975, | 154994,155171,155381, |
585 | 231 | 49 | 0 | 0 | 2 | 2 | 2 | 605 | ++ | NM_001086784 | 7393 | 896 | 1178 | ABRN02000389 | 948 | 20 | 905 | 5 | 53,126,36,32,33, | 896,949,1075,1112,1145, | 20,586,804,840,872, |
585 | 238 | 42 | 0 | 0 | 2 | 2 | 2 | 605 | ++ | NM_200976 | 7541 | 964 | 1246 | ABRN02000389 | 948 | 20 | 905 | 5 | 53,126,36,32,33, | 964,1017,1143,1180,1213, | 20,586,804,840,872, |
586 | 88 | 38 | 0 | 0 | 1 | 93 | 1 | 24877 | +- | NM_119096 | 1539 | 447 | 666 | JH474879 | 227703 | 140223 | 165226 | 2 | 60,66, | 447,600, | 62477,87414, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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