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Database: tarSyr2 Primary Table: xenoRefSeqAli Row Count: 375,108   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 | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 495 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 179 | 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 | 4 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 1336 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 4 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 2938 | 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_183166 | varchar(255) | values | Query sequence name |
qSize | 2852 | int(10) unsigned | range | Query sequence size |
qStart | 251 | int(10) unsigned | range | Alignment start position in query |
qEnd | 2261 | int(10) unsigned | range | Alignment end position in query |
tName | ABRT02000404v1 | varchar(255) | values | Target sequence name |
tSize | 5914 | int(10) unsigned | range | Target sequence size |
tStart | 140 | int(10) unsigned | range | Alignment start position in target |
tEnd | 3752 | int(10) unsigned | range | Alignment end position in target |
blockCount | 5 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 96,11,171,129,267, | longblob | | Size of each block |
qStarts | 251,523,1178,1496,1994, | longblob | | Start of each block in query. |
tStarts | 2162,2774,4778,5096,5507, | 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)
tarSyr2.all_mrna.qName (via xenoRefSeqAli.qName)
tarSyr2.xenoRefFlat.name (via xenoRefSeqAli.qName)
tarSyr2.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 |
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585 | 495 | 179 | 0 | 0 | 4 | 1336 | 4 | 2938 | +- | NM_183166 | 2852 | 251 | 2261 | ABRT02000404v1 | 5914 | 140 | 3752 | 5 | 96,11,171,129,267, | 251,523,1178,1496,1994, | 2162,2774,4778,5096,5507, |
585 | 1081 | 158 | 0 | 0 | 21 | 3687 | 20 | 2852 | +- | NM_001080488 | 7185 | 2240 | 7166 | KE928741v1 | 14488 | 7572 | 11663 | 25 | 84,15,57,36,27,84,66,44,36,12,69,80,81,6,14,39,234,30,57,22,21,5,12,81,27, | 2240,2349,2365,2434,2665,2741,2850,2997,3041,3082,3094,3252,3333,3433,3439,3738,5250,5535,5706,5806,5830,5861,5868,6184,7139, | 2825,2937,2952,3026,3241,3320,3420,3754,3799,3842,3855,3985,4065,4166,4173,4410,5325,5633,5765,5864,5886,5915,5920,6122,6889, |
585 | 526 | 74 | 0 | 0 | 3 | 82 | 2 | 74 | +- | NM_001033616 | 1956 | 183 | 865 | ABRT02000515v1 | 742 | 9 | 683 | 4 | 297,114,54,135, | 183,481,629,730, | 59,356,503,598, |
585 | 175 | 94 | 0 | 0 | 2 | 59 | 1 | 58 | +- | NM_001140623 | 942 | 210 | 538 | ABRT02000515v1 | 742 | 275 | 602 | 3 | 215,39,15, | 210,426,523, | 140,355,452, |
585 | 111 | 60 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001279004 | 592 | 133 | 304 | ABRT02000515v1 | 742 | 380 | 551 | 1 | 171, | 133, | 191, |
585 | 134 | 79 | 0 | 0 | 1 | 339 | 1 | 8347 | +- | NM_128579 | 1142 | 378 | 930 | KE926493v1 | 322470 | 101178 | 109738 | 2 | 99,114, | 378,816, | 212732,221178, |
586 | 595 | 269 | 0 | 0 | 2 | 39 | 2 | 25 | ++ | NM_100918 | 1347 | 217 | 1120 | KE936070v1 | 226324 | 169643 | 170532 | 3 | 345,444,75, | 217,577,1045, | 169643,169989,170457, |
585 | 83 | 46 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001248812 | 539 | 129 | 258 | ABRT02000515v1 | 742 | 410 | 539 | 1 | 129, | 129, | 203, |
586 | 746 | 415 | 0 | 0 | 6 | 1407 | 9 | 47958 | +- | NM_001313483 | 4331 | 1312 | 3880 | KE940975v1 | 894763 | 196726 | 245845 | 10 | 102,81,201,159,114,144,123,144,1,92, | 1312,1465,1546,1759,1930,3271,3439,3643,3787,3788, | 648918,649256,649455,649980,652162,688780,694947,697575,697725,697945, |
585 | 419 | 63 | 0 | 0 | 2 | 122 | 2 | 109 | ++ | NM_001133707 | 1902 | 39 | 643 | ABRT02000516v1 | 653 | 62 | 653 | 3 | 33,421,28, | 39,175,615, | 62,188,625, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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