|
|---|
| |
Database: caeRem2 Primary Table: xenoRefSeqAli Row Count: 271,110 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 | 870 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 66 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 24 | 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 | 1 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 21 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 1 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 273 | 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_001374790 | varchar(255) | values | Query sequence name |
| qSize | 6154 | int(10) unsigned | range | Query sequence size |
| qStart | 2264 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 2375 | int(10) unsigned | range | Alignment end position in query |
| tName | chrUn | varchar(255) | values | Target sequence name |
| tSize | 161944676 | int(10) unsigned | range | Target sequence size |
| tStart | 37455650 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 37456013 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 2 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 39,51, | longblob | | Size of each block |
| qStarts | 2264,2324, | longblob | | Start of each block in query. |
| tStarts | 37455650,37455962, | longblob | | Start of each block in target. |
|
| |
|
|
|
Connected Tables and Joining Fields
|
|---|
| |
caeRem2.all_est.qName (via xenoRefSeqAli.qName)
caeRem2.all_mrna.qName (via xenoRefSeqAli.qName)
caeRem2.xenoMrna.qName (via xenoRefSeqAli.qName)
caeRem2.xenoRefFlat.name (via xenoRefSeqAli.qName)
caeRem2.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)
| |
|
|
|
Sample Rows
|
|---|
| |
| bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
|---|
| 870 | 66 | 24 | 0 | 0 | 1 | 21 | 1 | 273 | ++ | NM_001374790 | 6154 | 2264 | 2375 | chrUn | 161944676 | 37455650 | 37456013 | 2 | 39,51, | 2264,2324, | 37455650,37455962, |
| 585 | 148 | 62 | 0 | 0 | 2 | 1089 | 2 | 1430 | ++ | NM_001172516 | 1767 | 198 | 1497 | chrUn | 161944676 | 17366 | 19006 | 3 | 39,45,126, | 198,1026,1371, | 17366,18487,18880, |
| 585 | 83 | 9 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_050163 | 203 | 0 | 92 | chrUn | 161944676 | 17497 | 17589 | 1 | 92, | 0, | 161927087, |
| 585 | 87 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_052824 | 100 | 0 | 95 | chrUn | 161944676 | 17497 | 17592 | 1 | 95, | 0, | 161927084, |
| 585 | 77 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_069188 | 100 | 0 | 80 | chrUn | 161944676 | 17510 | 17590 | 1 | 80, | 0, | 161927086, |
| 585 | 214 | 110 | 0 | 0 | 3 | 687 | 3 | 819 | ++ | NM_001079996 | 4676 | 463 | 1474 | chrUn | 161944676 | 17881 | 19024 | 4 | 84,75,84,81, | 463,610,970,1393, | 17881,18081,18472,18943, |
| 585 | 170 | 82 | 0 | 0 | 3 | 762 | 3 | 873 | ++ | NM_001034373 | 4259 | 747 | 1761 | chrUn | 161944676 | 17890 | 19015 | 4 | 75,36,69,72, | 747,903,1260,1689, | 17890,18099,18466,18943, |
| 585 | 179 | 79 | 0 | 0 | 3 | 750 | 3 | 867 | ++ | NM_001131773 | 3993 | 438 | 1446 | chrUn | 161944676 | 17890 | 19015 | 4 | 54,57,75,72, | 438,594,939,1374, | 17890,18099,18460,18943, |
| 809 | 340 | 101 | 0 | 0 | 1 | 20 | 1 | 48 | ++ | NM_003536 | 486 | 23 | 484 | chrUn | 161944676 | 29400154 | 29400643 | 2 | 417,24, | 23,460, | 29400154,29400619, |
| 1040 | 165 | 84 | 0 | 0 | 2 | 768 | 2 | 888 | ++ | NM_133969 | 2898 | 602 | 1619 | chrUn | 161944676 | 59673287 | 59674424 | 3 | 93,42,114, | 602,1133,1505, | 59673287,59673840,59674310, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|
US Server