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Database: proCap1 Primary Table: xenoRefSeqAli Row Count: 669,761 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 | description |
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| bin | 73 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| matches | 85084 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 9085 | 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 | 36 | int(10) unsigned | Number of 'N' bases |
| qNumInsert | 107 | int(10) unsigned | Number of inserts in query |
| qBaseInsert | 10093 | int(10) unsigned | Number of bases inserted in query |
| tNumInsert | 354 | int(10) unsigned | Number of inserts in target |
| tBaseInsert | 184350 | int(10) unsigned | Number of bases inserted in target |
| strand | +- | char(2) | + or - for strand. First character query, second target (optional) |
| qName | NM_001256850 | varchar(255) | Query sequence name |
| qSize | 104301 | int(10) unsigned | Query sequence size |
| qStart | 1 | int(10) unsigned | Alignment start position in query |
| qEnd | 104299 | int(10) unsigned | Alignment end position in query |
| tName | scaffold_0 | varchar(255) | Target sequence name |
| tSize | 380827 | int(10) unsigned | Target sequence size |
| tStart | 6225 | int(10) unsigned | Alignment start position in target |
| tEnd | 284780 | int(10) unsigned | Alignment end position in target |
| blockCount | 379 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 17,172,109,293,48,142,131,4... | longblob | Size of each block |
| qStarts | 1,19,210,518,1077,1137,1282... | longblob | Start of each block in query. |
| tStarts | 96047,96064,98423,103188,10... | 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)
proCap1.xenoRefFlat.name (via xenoRefSeqAli.qName)
proCap1.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 | 85084 | 9085 | 0 | 36 | 107 | 10093 | 354 | 184350 | +- | NM_001256850 | 104301 | 1 | 104299 | scaffold_0 | 380827 | 6225 | 284780 | 379 | 17,172,109,293,48,142,131,45,155,75,58,100,23,74,153,146,286,123,282,66,259,64,216,143,206,234,245,181,48,1327,82,21,32,106,266, ... | 1,19,210,518,1077,1137,1282,1425,1470,1625,1703,1761,1861,1936,2010,2163,2309,2595,2718,3000,3066,3325,3389,3605,3748,3954,4188, ... | 96047,96064,98423,103188,104062,107152,107294,107425,107814,108942,109017,110442,110548,111663,112322,112978,116484,116877,11865 ... |
| 73 | 66882 | 6831 | 0 | 36 | 72 | 8277 | 223 | 204806 | +- | NM_003319 | 82029 | 1 | 82027 | scaffold_0 | 380827 | 6225 | 284780 | 242 | 17,172,109,293,48,142,131,45,155,75,58,100,22,4,138,146,286,123,282,66,259,64,216,143,206,234,245,181,48,1327,82,21,32,106,266,2 ... | 1,19,210,518,1077,1137,1282,1425,1470,1625,1703,1761,1861,1883,1887,2025,2171,2457,2580,2862,2928,3187,3251,3467,3610,3816,4050, ... | 96047,96064,98423,103188,104062,107152,107294,107425,107814,108942,109017,110442,110548,110594,112337,112978,116484,116877,11865 ... |
| 73 | 84041 | 8871 | 0 | 36 | 103 | 8569 | 349 | 185607 | +- | NM_133378 | 101520 | 1 | 101518 | scaffold_0 | 380827 | 6225 | 284780 | 374 | 17,172,109,293,48,142,131,45,155,75,58,100,23,74,153,146,286,123,282,66,259,64,216,143,206,234,245,181,48,1327,82,21,32,106,266, ... | 1,19,210,518,1077,1137,1282,1425,1470,1625,1703,1761,1861,1936,2010,2163,2309,2595,2718,3000,3066,3325,3389,3605,3748,3954,4188, ... | 96047,96064,98423,103188,104062,107152,107294,107425,107814,108942,109017,110442,110548,111663,112322,112978,116484,116877,11865 ... |
| 73 | 67232 | 6856 | 0 | 36 | 72 | 8277 | 224 | 204431 | +- | NM_133432 | 82404 | 1 | 82402 | scaffold_0 | 380827 | 6225 | 284780 | 243 | 17,172,109,293,48,142,131,45,155,75,58,100,22,4,138,146,286,123,282,66,259,64,216,143,206,234,245,181,48,1327,82,21,32,106,266,2 ... | 1,19,210,518,1077,1137,1282,1425,1470,1625,1703,1761,1861,1883,1887,2025,2171,2457,2580,2862,2928,3187,3251,3467,3610,3816,4050, ... | 96047,96064,98423,103188,104062,107152,107294,107425,107814,108942,109017,110442,110548,110594,112337,112978,116484,116877,11865 ... |
| 73 | 67153 | 6885 | 0 | 36 | 74 | 8528 | 225 | 204481 | +- | NM_133437 | 82605 | 1 | 82603 | scaffold_0 | 380827 | 6225 | 284780 | 244 | 17,172,109,293,48,142,131,45,155,75,58,100,22,4,138,146,286,123,282,66,259,64,216,143,206,234,245,181,48,1327,82,21,32,106,266,2 ... | 1,19,210,518,1077,1137,1282,1425,1470,1625,1703,1761,1861,1883,1887,2025,2171,2457,2580,2862,2928,3187,3251,3467,3610,3816,4050, ... | 96047,96064,98423,103188,104062,107152,107294,107425,107814,108942,109017,110442,110548,110594,112337,112978,116484,116877,11865 ... |
| 73 | 79319 | 12641 | 0 | 39 | 131 | 9675 | 357 | 186555 | +- | NM_011652 | 101674 | 0 | 101674 | scaffold_0 | 380827 | 6227 | 284781 | 383 | 47,142,109,294,48,144,135,156,77,140,145,135,299,121,164,118,66,259,25,27,216,143,206,234,247,41,142,48,1327,83,17,65,108,267,27 ... | 0,47,208,515,1072,1132,1279,1463,1619,1753,2019,2164,2299,2598,2719,2889,3007,3073,3332,3365,3393,3609,3752,3958,4192,4439,4492, ... | 96046,96094,98423,103187,104062,107152,107296,107812,108941,110439,112330,112978,116473,116879,118651,118815,119198,119991,12059 ... |
| 73 | 63303 | 9769 | 0 | 39 | 87 | 8820 | 229 | 205443 | +- | NM_028004 | 81931 | 0 | 81931 | scaffold_0 | 380827 | 6227 | 284781 | 244 | 47,142,109,294,48,144,135,156,77,139,134,135,299,121,164,118,66,259,25,27,216,143,206,234,247,41,142,48,1327,83,17,65,108,267,27 ... | 0,47,208,515,1072,1132,1279,1463,1619,1753,1892,2026,2161,2460,2581,2751,2869,2935,3194,3227,3255,3471,3614,3820,4054,4301,4354, ... | 96046,96094,98423,103187,104062,107152,107296,107812,108941,110439,112341,112978,116473,116879,118651,118815,119198,119991,12059 ... |
| 585 | 1557 | 287 | 0 | 0 | 14 | 2948 | 23 | 24859 | +- | NM_001320674 | 6147 | 50 | 4842 | scaffold_2021 | 97678 | 16908 | 43611 | 25 | 136,104,3,70,179,104,131,87,99,36,106,82,91,82,63,108,108,11,9,16,69,18,36,66,30, | 50,186,290,293,536,715,819,950,1037,1136,1172,1278,1365,1472,1564,1631,2032,2402,2801,2820,2852,3212,4404,4506,4812, | 54067,65859,66126,67030,69220,72055,72770,74168,74355,75450,77980,78103,78185,78284,78373,78439,78792,79171,79580,79598,79636,79 ... |
| 585 | 174 | 96 | 0 | 0 | 1 | 144 | 1 | 1139 | +- | NM_001139755 | 2490 | 1001 | 1415 | scaffold_0 | 380827 | 7247 | 8656 | 2 | 123,147, | 1001,1268, | 372171,373433, |
| 585 | 80 | 49 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001097828 | 3086 | 905 | 1034 | scaffold_0 | 380827 | 15145 | 15274 | 1 | 129, | 905, | 365553, |
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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