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Database: thaSir1 Primary Table: xenoRefSeqAli Row Count: 447,067 Data last updated: 2018-07-31
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 | 2192 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 646 | 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 | 8 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 705 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 23 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 12147 | 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_001244536 | varchar(255) | values | Query sequence name |
| qSize | 5815 | int(10) unsigned | range | Query sequence size |
| qStart | 258 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 3801 | int(10) unsigned | range | Alignment end position in query |
| tName | NW_013657680v1 | varchar(255) | values | Target sequence name |
| tSize | 3920154 | int(10) unsigned | range | Target sequence size |
| tStart | 51639 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 66624 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 24 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 51,215,76,54,93,169,4,171,4... | longblob | | Size of each block |
| qStarts | 258,585,800,921,1206,1305,1... | longblob | | Start of each block in query. |
| tStarts | 3853530,3853872,3854658,385... | 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)
thaSir1.all_mrna.qName (via xenoRefSeqAli.qName)
thaSir1.xenoRefFlat.name (via xenoRefSeqAli.qName)
thaSir1.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 | 2192 | 646 | 0 | 0 | 8 | 705 | 23 | 12147 | +- | NM_001244536 | 5815 | 258 | 3801 | NW_013657680v1 | 3920154 | 51639 | 66624 | 24 | 51,215,76,54,93,169,4,171,4,170,4,124,155,217,41,163,117,235,230,268,96,138,22,21, | 258,585,800,921,1206,1305,1474,1478,1649,1653,1823,1827,1951,2106,2323,2432,2595,2712,2947,3179,3447,3543,3728,3780, | 3853530,3853872,3854658,3855236,3858119,3858990,3859167,3859606,3859835,3859975,3860303,3860430,3860650,3861633,3862400,3863051, ... |
| 585 | 2298 | 501 | 0 | 0 | 8 | 608 | 21 | 12006 | +- | NM_001199453 | 5994 | 321 | 3728 | NW_013657680v1 | 3920154 | 51721 | 66526 | 22 | 42,25,162,69,78,93,169,4,173,170,124,155,219,39,162,117,235,230,270,95,139,29, | 321,399,622,784,874,1183,1282,1451,1455,1628,1804,1928,2083,2302,2410,2572,2689,2924,3154,3424,3519,3699, | 3853628,3853706,3853932,3854665,3855215,3858119,3858990,3859167,3859606,3859973,3860430,3860650,3861633,3862402,3863052,3863687, ... |
| 590 | 121 | 32 | 0 | 0 | 1 | 30 | 1 | 30 | +- | NM_001364696 | 1197 | 254 | 437 | NW_013657954v1 | 1028205 | 774959 | 775142 | 2 | 30,123, | 254,314, | 253063,253123, |
| 73 | 1935 | 464 | 0 | 22 | 3 | 92 | 27 | 209268 | +- | NM_001204809 | 3037 | 62 | 2575 | NW_013657955v1 | 1026012 | 125675 | 337364 | 28 | 42,75,80,100,111,99,139,145,101,101,3,145,87,57,95,57,3,195,101,53,3,50,133,110,176,73,6,81, | 62,127,217,297,397,508,607,746,891,992,1093,1096,1241,1328,1385,1480,1537,1540,1735,1836,1889,1892,1942,2075,2239,2415,2488,2494 ... | 688648,689188,700417,701288,701833,739975,741179,755759,756012,756919,757038,757484,759459,765510,773284,773456,773519,773645,77 ... |
| 585 | 2084 | 580 | 0 | 0 | 8 | 829 | 21 | 12237 | +- | NM_003246 | 7253 | 257 | 3750 | NW_013657680v1 | 3920154 | 51723 | 66624 | 22 | 51,222,69,54,93,169,4,171,4,170,4,126,217,41,163,117,235,230,268,98,136,22, | 257,584,806,920,1205,1304,1473,1477,1648,1652,1822,1826,2105,2322,2431,2594,2711,2946,3178,3446,3544,3728, | 3853530,3853872,3854665,3855236,3858119,3858990,3859167,3859606,3859835,3859975,3860303,3860430,3861633,3862400,3863051,3863687, ... |
| 585 | 2169 | 637 | 0 | 0 | 7 | 687 | 25 | 12095 | +- | NM_174196 | 5269 | 225 | 3718 | NW_013657680v1 | 3920154 | 51723 | 66624 | 26 | 48,10,29,222,69,93,169,4,171,4,170,4,124,155,217,41,160,3,117,235,230,2,268,95,144,22, | 225,333,510,552,774,1173,1272,1441,1445,1616,1620,1790,1794,1918,2073,2290,2399,2559,2562,2679,2914,3144,3146,3414,3509,3696, | 3853530,3853650,3853827,3853872,3854665,3858119,3858990,3859167,3859606,3859835,3859975,3860283,3860430,3860650,3861633,3862400, ... |
| 585 | 1633 | 611 | 0 | 0 | 6 | 810 | 17 | 11786 | +- | NM_001163128 | 3651 | 462 | 3516 | NW_013657680v1 | 3920154 | 52192 | 66222 | 18 | 48,78,90,168,170,2,173,217,41,160,121,232,2,229,2,268,98,145, | 462,618,1029,1131,1305,1475,1477,1932,2149,2259,2419,2540,2772,2774,3003,3005,3273,3371, | 3853932,3854659,3858119,3858990,3859607,3859831,3859973,3861633,3862400,3863052,3863685,3865266,3865521,3866127,3866380,3867088, ... |
| 585 | 1780 | 641 | 0 | 0 | 6 | 657 | 17 | 11651 | +- | NM_001163118 | 3561 | 417 | 3495 | NW_013657680v1 | 3920154 | 52195 | 66267 | 18 | 93,84,90,169,5,170,4,168,126,217,41,160,121,233,236,264,96,144, | 417,606,1011,1113,1282,1287,1457,1461,1635,1914,2131,2241,2401,2522,2755,2991,3255,3351, | 3853887,3854653,3858119,3858990,3859339,3859607,3859835,3859975,3860430,3861633,3862400,3863052,3863685,3865266,3866126,3867092, ... |
| 585 | 1810 | 670 | 0 | 0 | 5 | 615 | 18 | 11591 | +- | NM_001279737 | 3641 | 417 | 3512 | NW_013657680v1 | 3920154 | 52196 | 66267 | 19 | 132,78,87,169,5,172,2,171,153,217,41,160,119,235,230,2,268,95,144, | 417,618,1029,1131,1300,1305,1477,1479,1779,1932,2149,2259,2419,2538,2773,3003,3005,3273,3368, | 3853887,3854659,3858119,3858990,3859339,3859607,3859837,3859975,3860652,3861633,3862400,3863052,3863685,3865264,3866126,3866380, ... |
| 585 | 2267 | 708 | 0 | 0 | 5 | 362 | 22 | 11350 | +- | NM_001013062 | 3734 | 200 | 3537 | NW_013657680v1 | 3920154 | 52200 | 66525 | 23 | 228,215,76,54,93,169,4,173,2,170,4,124,155,217,41,161,119,235,230,2,268,95,140, | 200,440,655,776,1061,1160,1329,1333,1506,1508,1678,1682,1806,1961,2178,2287,2448,2567,2802,3032,3034,3302,3397, | 3853629,3853872,3854658,3855236,3858119,3858990,3859167,3859606,3859837,3859975,3860303,3860430,3860650,3861633,3862400,3863051, ... |
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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