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Database: panTro1 Primary Table: xenoRefSeqAli Row Count: 508,887 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 | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| matches | 1603 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 34 | 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 | 15 | int(10) unsigned | Number of bases inserted in query |
| tNumInsert | 12 | int(10) unsigned | Number of inserts in target |
| tBaseInsert | 914 | int(10) unsigned | Number of bases inserted in target |
| strand | ++ | char(2) | + or - for strand. First character query, second target (optional) |
| qName | NR_034090 | varchar(255) | Query sequence name |
| qSize | 1652 | int(10) unsigned | Query sequence size |
| qStart | 0 | int(10) unsigned | Alignment start position in query |
| qEnd | 1652 | int(10) unsigned | Alignment end position in query |
| tName | chr1 | varchar(255) | Target sequence name |
| tSize | 229575298 | int(10) unsigned | Target sequence size |
| tStart | 1745 | int(10) unsigned | Alignment start position in target |
| tEnd | 4296 | int(10) unsigned | Alignment end position in target |
| blockCount | 13 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 354,109,38,541,265,7,25,12,... | longblob | Size of each block |
| qStarts | 0,354,463,501,1042,1307,131... | longblob | Start of each block in query. |
| tStarts | 1745,2483,3091,3130,3673,39... | 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)
panTro1.all_est.qName (via xenoRefSeqAli.qName)
panTro1.all_mrna.qName (via xenoRefSeqAli.qName)
panTro1.refGene.name (via xenoRefSeqAli.qName)
panTro1.refSeqAli.qName (via xenoRefSeqAli.qName)
panTro1.xenoMrna.qName (via xenoRefSeqAli.qName)
panTro1.xenoRefFlat.name (via xenoRefSeqAli.qName)
panTro1.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 | 1603 | 34 | 0 | 0 | 1 | 15 | 12 | 914 | ++ | NR_034090 | 1652 | 0 | 1652 | chr1 | 229575298 | 1745 | 4296 | 13 | 354,109,38,541,265,7,25,12,15,9,6,3,253, | 0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399, | 1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043, |
| 585 | 1596 | 31 | 0 | 0 | 1 | 25 | 12 | 924 | ++ | NR_045117 | 1652 | 0 | 1652 | chr1 | 229575298 | 1745 | 4296 | 13 | 354,109,38,541,265,7,15,12,15,9,6,3,253, | 0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399, | 1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043, |
| 585 | 1603 | 34 | 0 | 0 | 1 | 15 | 12 | 914 | ++ | NR_046018 | 1652 | 0 | 1652 | chr1 | 229575298 | 1745 | 4296 | 13 | 354,109,38,541,265,7,25,12,15,9,6,3,253, | 0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399, | 1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043, |
| 585 | 1443 | 30 | 0 | 0 | 1 | 15 | 11 | 1078 | ++ | NR_051985 | 1488 | 0 | 1488 | chr1 | 229575298 | 1745 | 4296 | 12 | 354,127,397,265,7,25,12,15,9,6,3,253, | 0,354,481,878,1143,1150,1190,1202,1217,1226,1232,1235, | 1745,2465,3274,3673,3939,3948,3992,4005,4022,4032,4039,4043, |
| 585 | 1600 | 40 | 0 | 0 | 1 | 15 | 12 | 914 | ++ | NR_051986 | 1655 | 0 | 1655 | chr1 | 229575298 | 1745 | 4299 | 13 | 354,109,38,541,265,7,25,12,15,9,6,3,256, | 0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399, | 1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043, |
| 585 | 1558 | 35 | 0 | 0 | 2 | 50 | 11 | 961 | ++ | NR_110561 | 1643 | 0 | 1643 | chr1 | 229575298 | 1745 | 4299 | 12 | 354,109,38,541,263,12,15,9,5,3,102,142, | 0,354,463,501,1042,1354,1366,1381,1391,1396,1399,1501, | 1745,2483,3091,3130,3673,3992,4005,4022,4033,4039,4043,4157, |
| 585 | 102 | 36 | 0 | 0 | 1 | 108 | 2 | 939 | ++ | NM_001007319 | 3753 | 2433 | 2679 | chr1 | 229575298 | 2052 | 3129 | 3 | 45,55,38, | 2433,2586,2641, | 2052,2868,3091, |
| 585 | 157 | 56 | 0 | 0 | 1 | 33 | 3 | 864 | ++ | NM_001170825 | 3694 | 3087 | 3333 | chr1 | 229575298 | 2052 | 3129 | 4 | 44,88,43,38, | 3087,3131,3252,3295, | 2052,2480,2880,3091, |
| 585 | 1614 | 25 | 0 | 0 | 2 | 83 | 18 | 14374 | +- | NR_024540 | 1786 | 47 | 1769 | chr1 | 229575298 | 4248 | 20261 | 19 | 152,46,23,35,147,137,136,78,61,59,16,106,42,62,71,134,184,56,94, | 47,199,245,268,303,450,587,723,801,862,921,974,1080,1122,1230,1301,1435,1619,1675, | 229555037,229560708,229560755,229560779,229561021,229567037,229567413,229567726,229567805,229567867,229568018,229568080,22956884 ... |
| 585 | 2003 | 42 | 0 | 0 | 4 | 261 | 21 | 18961 | +- | NR_003659 | 2590 | 248 | 2554 | chr1 | 229575298 | 4248 | 25254 | 22 | 157,144,99,152,46,23,35,147,9,124,136,78,61,63,16,106,105,71,134,184,61,94, | 248,405,575,826,978,1024,1047,1082,1229,1238,1362,1498,1576,1637,1700,1753,1859,2010,2081,2215,2399,2460, | 229550044,229550202,229550365,229555037,229560708,229560755,229560779,229561021,229567037,229567050,229567413,229567726,22956780 ... |
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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