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Database: neoSch1 Primary Table: xenoRefSeqAli Row Count: 446,526   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 | 230 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 70 | 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 | 0 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 0 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 2 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 6678 | 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_001006460 | varchar(255) | values | Query sequence name |
qSize | 2005 | int(10) unsigned | range | Query sequence size |
qStart | 300 | int(10) unsigned | range | Alignment start position in query |
qEnd | 600 | int(10) unsigned | range | Alignment end position in query |
tName | NW_018726556v1 | varchar(255) | values | Target sequence name |
tSize | 10277 | int(10) unsigned | range | Target sequence size |
tStart | 3140 | int(10) unsigned | range | Alignment start position in target |
tEnd | 10118 | int(10) unsigned | range | Alignment end position in target |
blockCount | 3 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 35,115,150, | longblob | | Size of each block |
qStarts | 300,335,450, | longblob | | Start of each block in query. |
tStarts | 3140,8875,9968, | 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)
neoSch1.xenoRefFlat.name (via xenoRefSeqAli.qName)
neoSch1.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 |
---|
585 | 230 | 70 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001006460 | 2005 | 300 | 600 | NW_018726556v1 | 10277 | 3140 | 10118 | 3 | 35,115,150, | 300,335,450, | 3140,8875,9968, |
585 | 228 | 72 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001085698 | 803 | 267 | 567 | NW_018726556v1 | 10277 | 3140 | 10118 | 3 | 36,114,150, | 267,303,417, | 3140,8876,9968, |
585 | 222 | 78 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001102769 | 879 | 307 | 607 | NW_018726556v1 | 10277 | 3140 | 10118 | 3 | 36,114,150, | 307,343,457, | 3140,8876,9968, |
585 | 227 | 73 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001245818 | 971 | 196 | 496 | NW_018726556v1 | 10277 | 3140 | 10118 | 3 | 36,114,150, | 196,232,346, | 3140,8876,9968, |
585 | 289 | 31 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001076256 | 1084 | 307 | 627 | NW_018726556v1 | 10277 | 3140 | 10138 | 3 | 35,115,170, | 307,342,457, | 3140,8875,9968, |
585 | 288 | 32 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001308570 | 1021 | 301 | 621 | NW_018726556v1 | 10277 | 3140 | 10138 | 3 | 35,115,170, | 301,336,451, | 3140,8875,9968, |
585 | 280 | 40 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_010753 | 1194 | 296 | 616 | NW_018726556v1 | 10277 | 3140 | 10138 | 3 | 35,115,170, | 296,331,446, | 3140,8875,9968, |
585 | 1921 | 331 | 0 | 0 | 0 | 0 | 7 | 5144 | ++ | NM_198055 | 2666 | 279 | 2531 | NW_018734339v1 | 738612 | 39284 | 46680 | 8 | 438,185,4,66,121,245,395,798, | 279,717,902,906,972,1093,1338,1733, | 39284,40165,40551,41042,41223,45227,45478,45882, |
585 | 221 | 76 | 0 | 0 | 0 | 0 | 2 | 6678 | ++ | NM_001090987 | 934 | 413 | 710 | NW_018726556v1 | 10277 | 3143 | 10118 | 3 | 33,114,150, | 413,446,560, | 3143,8876,9968, |
585 | 241 | 38 | 0 | 0 | 0 | 0 | 1 | 978 | ++ | NM_001108364 | 1185 | 289 | 568 | NW_018726556v1 | 10277 | 8873 | 10130 | 2 | 117,162, | 289,406, | 8873,9968, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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