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Database: echTel2 Primary Table: xenoRefSeqAli Row Count: 470,748 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 |
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| bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 611 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 114 | 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 | 3 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 282 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 6 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 11120 | 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_022814 | varchar(255) | values | Query sequence name |
| qSize | 11275 | int(10) unsigned | range | Query sequence size |
| qStart | 10268 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 11275 | int(10) unsigned | range | Alignment end position in query |
| tName | AAIY02265372 | varchar(255) | values | Target sequence name |
| tSize | 16022 | int(10) unsigned | range | Target sequence size |
| tStart | 3481 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 15326 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 177,169,99,94,96,30,60, | longblob | | Size of each block |
| qStarts | 10268,10445,10614,10714,108... | longblob | | Start of each block in query. |
| tStarts | 696,2863,4921,6399,9208,123... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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echTel2.xenoRefFlat.name (via xenoRefSeqAli.qName)
echTel2.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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| 585 | 611 | 114 | 0 | 0 | 3 | 282 | 6 | 11120 | +- | NM_022814 | 11275 | 10268 | 11275 | AAIY02265372 | 16022 | 3481 | 15326 | 7 | 177,169,99,94,96,30,60, | 10268,10445,10614,10714,10808,11110,11215, | 696,2863,4921,6399,9208,12377,12481, |
| 585 | 72 | 30 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001096157 | 2275 | 341 | 443 | AAIY02265762 | 12879 | 619 | 721 | 1 | 102, | 341, | 619, |
| 585 | 229 | 107 | 0 | 0 | 1 | 279 | 1 | 2561 | ++ | NM_001094784 | 1894 | 423 | 1038 | AAIY02265762 | 12879 | 619 | 3516 | 2 | 102,234, | 423,804, | 619,3282, |
| 585 | 220 | 116 | 0 | 0 | 1 | 282 | 1 | 2561 | ++ | NM_001097849 | 2155 | 381 | 999 | AAIY02265762 | 12879 | 619 | 3516 | 2 | 102,234, | 381,765, | 619,3282, |
| 585 | 214 | 101 | 0 | 0 | 2 | 269 | 2 | 1000 | ++ | NM_001002087 | 2059 | 371 | 955 | AAIY02265762 | 12879 | 2994 | 4309 | 3 | 126,171,18, | 371,704,937, | 2994,3345,4291, |
| 585 | 79 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001257589 | 5356 | 2 | 89 | AAIY02266072 | 10912 | 165 | 252 | 1 | 87, | 2, | 10660, |
| 634 | 247 | 42 | 0 | 0 | 0 | 0 | 1 | 111 | +- | NM_144638 | 977 | 204 | 493 | JH980325 | 24928835 | 6473342 | 6473742 | 2 | 148,141, | 204,352, | 18455093,18455352, |
| 585 | 61 | 20 | 0 | 0 | 1 | 6 | 1 | 144 | +- | NR_050566 | 93 | 1 | 88 | AAIY02266072 | 10912 | 996 | 1221 | 2 | 66,15, | 1,73, | 9691,9901, |
| 585 | 73 | 26 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NR_052805 | 102 | 1 | 100 | AAIY02266072 | 10912 | 1193 | 1292 | 1 | 99, | 1, | 1193, |
| 585 | 728 | 94 | 0 | 0 | 0 | 0 | 4 | 7125 | +- | NM_010889 | 22489 | 8840 | 9662 | AAIY02266928 | 7949 | 2 | 7949 | 5 | 249,204,105,108,156, | 8840,9089,9293,9398,9506, | 0,667,1300,5362,7791, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server