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Database: micMur1 Primary Table: xenoRefSeqAli Row Count: 681,359 Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 73 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| matches | 3613 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 543 | 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 | 1 | int(10) unsigned | Number of inserts in query |
| qBaseInsert | 119 | int(10) unsigned | Number of bases inserted in query |
| tNumInsert | 21 | int(10) unsigned | Number of inserts in target |
| tBaseInsert | 194898 | int(10) unsigned | Number of bases inserted in target |
| strand | ++ | char(2) | + or - for strand. First character query, second target (optional) |
| qName | NM_001107939 | varchar(255) | Query sequence name |
| qSize | 4933 | int(10) unsigned | Query sequence size |
| qStart | 111 | int(10) unsigned | Alignment start position in query |
| qEnd | 4386 | int(10) unsigned | Alignment end position in query |
| tName | scaffold_0 | varchar(255) | Target sequence name |
| tSize | 1949650 | int(10) unsigned | Target sequence size |
| tStart | 198887 | int(10) unsigned | Alignment start position in target |
| tEnd | 397941 | int(10) unsigned | Alignment end position in target |
| blockCount | 22 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 1068,146,294,194,500,4,127,... | longblob | Size of each block |
| qStarts | 111,1179,1325,1619,1932,243... | longblob | Start of each block in query. |
| tStarts | 198887,223078,227386,234900... | 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)
micMur1.all_mrna.qName (via xenoRefSeqAli.qName)
micMur1.xenoRefFlat.name (via xenoRefSeqAli.qName)
micMur1.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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| 73 | 3613 | 543 | 0 | 0 | 1 | 119 | 21 | 194898 | ++ | NM_001107939 | 4933 | 111 | 4386 | scaffold_0 | 1949650 | 198887 | 397941 | 22 | 1068,146,294,194,500,4,127,2,89,2,192,109,99,214,171,125,211,172,148,107,75,107, | 111,1179,1325,1619,1932,2432,2436,2563,2565,2654,2656,2848,2957,3056,3270,3441,3566,3777,3949,4097,4204,4279, | 198887,223078,227386,234900,248618,251109,280353,280515,285532,285868,316402,346380,347430,349902,358932,361408,369398,370309,37 ... |
| 73 | 4722 | 725 | 0 | 0 | 18 | 4586 | 39 | 212072 | ++ | NM_021362 | 11027 | 769 | 10802 | scaffold_0 | 1949650 | 198887 | 416406 | 41 | 1068,146,294,194,503,128,2,89,2,192,109,141,214,171,182,211,172,148,107,75,107,92,181,130,30,19,14,14,19,27,42,13,171,11,14,96,2 ... | 769,1837,1983,2277,2590,3093,3221,3223,3312,3314,3506,3615,3756,3970,4141,4323,4534,4706,4854,4961,5036,5929,6022,6281,6411,6785 ... | 198887,223078,227386,234900,248618,280352,280515,285532,285868,316402,346380,347430,349902,358932,361408,369398,370309,378692,38 ... |
| 585 | 1495 | 213 | 0 | 0 | 21 | 975 | 23 | 3899 | ++ | NR_134458 | 3038 | 355 | 3038 | scaffold_4012 | 178811 | 85832 | 91439 | 28 | 146,193,40,123,24,11,37,18,21,4,230,98,30,53,80,37,31,39,27,49,14,104,9,10,169,24,54,33, | 355,501,695,781,915,939,994,1383,1431,1453,1457,1703,1944,1976,2029,2119,2328,2374,2444,2471,2522,2554,2677,2700,2717,2923,2951, ... | 85832,87549,87742,87794,87940,87965,88029,88094,88144,88165,88177,88433,90521,90551,90605,90690,90727,90772,90840,90873,90926,90 ... |
| 585 | 150 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_135541 | 7745 | 1472 | 1634 | scaffold_51215 | 5792 | 61 | 223 | 1 | 162, | 1472, | 5569, |
| 585 | 150 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_135543 | 7412 | 1139 | 1301 | scaffold_51215 | 5792 | 61 | 223 | 1 | 162, | 1139, | 5569, |
| 585 | 150 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_135544 | 7853 | 1472 | 1634 | scaffold_51215 | 5792 | 61 | 223 | 1 | 162, | 1472, | 5569, |
| 9 | 98 | 14 | 0 | 0 | 2 | 338 | 3 | 830463 | +- | NM_173450 | 5135 | 2355 | 2805 | scaffold_0 | 1949650 | 334974 | 1165549 | 4 | 40,24,26,22, | 2355,2719,2757,2783, | 784101,999151,1404176,1614654, |
| 73 | 76 | 10 | 0 | 0 | 1 | 304 | 3 | 267511 | +- | NM_001107641 | 7666 | 6582 | 6972 | scaffold_0 | 1949650 | 334978 | 602575 | 4 | 22,4,33,27, | 6582,6604,6608,6945, | 1347075,1347841,1404846,1614645, |
| 585 | 277 | 33 | 0 | 0 | 1 | 25 | 3 | 25 | ++ | NR_134459 | 827 | 355 | 690 | scaffold_4012 | 178811 | 72332 | 72667 | 4 | 23,165,83,39, | 355,378,568,651, | 72332,72357,72544,72628, |
| 588 | 308 | 43 | 0 | 0 | 7 | 356 | 6 | 362 | ++ | NM_021362 | 11027 | 8478 | 9185 | scaffold_0 | 1949650 | 417031 | 417744 | 8 | 85,35,5,37,18,132,15,24, | 8478,8710,8746,8754,8848,8883,9087,9161, | 417031,417237,417274,417279,417375,417415,417627,417720, |
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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