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Database: loxAfr3 Primary Table: xenoRefSeqAli Row Count: 359,460   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 573 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 104 | 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 | 13 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 1065 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 11 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 754 | 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_001193634 | varchar(255) | values | Query sequence name |
qSize | 1759 | int(10) unsigned | range | Query sequence size |
qStart | 13 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1755 | int(10) unsigned | range | Alignment end position in query |
tName | chrM | varchar(255) | values | Target sequence name |
tSize | 16866 | int(10) unsigned | range | Target sequence size |
tStart | 1162 | int(10) unsigned | range | Alignment start position in target |
tEnd | 2593 | int(10) unsigned | range | Alignment end position in target |
blockCount | 14 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 27,25,42,24,51,13,27,5,18,1... | longblob | | Size of each block |
qStarts | 13,129,162,230,445,545,565,... | longblob | | Start of each block in query. |
tStarts | 1162,1276,1308,1376,1596,17... | 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)
loxAfr3.all_mrna.qName (via xenoRefSeqAli.qName)
loxAfr3.refGene.name (via xenoRefSeqAli.qName)
loxAfr3.refSeqAli.qName (via xenoRefSeqAli.qName)
loxAfr3.xenoMrna.qName (via xenoRefSeqAli.qName)
loxAfr3.xenoRefFlat.name (via xenoRefSeqAli.qName)
loxAfr3.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 | 573 | 104 | 0 | 0 | 13 | 1065 | 11 | 754 | ++ | NM_001193634 | 1759 | 13 | 1755 | chrM | 16866 | 1162 | 2593 | 14 | 27,25,42,24,51,13,27,5,18,116,57,21,100,151, | 13,129,162,230,445,545,565,595,610,642,775,1076,1503,1604, | 1162,1276,1308,1376,1596,1702,1720,1747,1764,1794,1928,2231,2342,2442, |
638 | 1275 | 219 | 0 | 0 | 12 | 1474 | 14 | 1751 | ++ | NR_148919 | 3109 | 139 | 3107 | scaffold_26 | 35828716 | 7032541 | 7035786 | 17 | 96,256,16,51,172,51,109,93,19,66,44,83,44,11,132,87,164, | 139,242,533,628,746,1020,1347,1456,2172,2302,2410,2455,2538,2582,2602,2856,2943, | 7032541,7032643,7032933,7032994,7033105,7033876,7034421,7034533,7034872,7034995,7035094,7035138,7035223,7035268,7035279,7035531, ... |
107 | 872 | 224 | 0 | 0 | 4 | 584 | 7 | 12734 | +- | NM_001348269 | 2883 | 106 | 1786 | scaffold_4 | 100893473 | 36300926 | 36314756 | 8 | 187,142,156,293,139,48,14,117, | 106,351,493,649,942,1505,1641,1669, | 64578717,64588109,64588852,64591092,64591391,64592177,64592401,64592430, |
797 | 1194 | 168 | 0 | 0 | 9 | 792 | 11 | 11240 | ++ | NM_001003170 | 2534 | 252 | 2406 | scaffold_9 | 83325590 | 27815278 | 27827880 | 12 | 39,570,243,72,90,56,36,60,105,9,46,36, | 252,297,867,1120,1377,1777,1841,1914,2072,2177,2187,2370, | 27815278,27815329,27826297,27826547,27826804,27827230,27827291,27827366,27827521,27827638,27827650,27827844, |
585 | 671 | 85 | 0 | 0 | 12 | 636 | 11 | 640 | ++ | NM_001194967 | 1433 | 41 | 1433 | chrM | 16866 | 1171 | 2567 | 13 | 54,52,13,30,78,51,8,44,10,24,110,54,228, | 41,118,177,192,249,464,570,584,629,715,743,1096,1205, | 1171,1250,1308,1322,1379,1596,1707,1719,1763,1850,1877,2231,2339, |
585 | 427 | 66 | 0 | 0 | 6 | 719 | 6 | 720 | ++ | NM_001190487 | 1395 | 183 | 1395 | chrM | 16866 | 1313 | 2526 | 7 | 39,31,57,142,24,13,187, | 183,295,465,707,1105,1193,1208, | 1313,1425,1596,1837,2238,2325,2339, |
585 | 464 | 63 | 0 | 0 | 13 | 667 | 14 | 673 | ++ | NM_001190489 | 1494 | 207 | 1401 | chrM | 16866 | 1377 | 2577 | 16 | 21,25,15,13,7,15,45,23,5,33,18,46,30,42,105,84, | 207,261,368,385,506,519,539,676,700,705,747,765,1055,1161,1206,1317, | 1377,1431,1539,1555,1686,1700,1718,1850,1873,1879,1922,1941,2231,2339,2385,2493, |
585 | 248 | 46 | 0 | 0 | 2 | 819 | 2 | 820 | ++ | NM_001193643 | 1560 | 317 | 1430 | chrM | 16866 | 1425 | 2539 | 3 | 30,66,198, | 317,809,1232, | 1425,1918,2341, |
828 | 153 | 42 | 0 | 0 | 2 | 723 | 2 | 2609 | ++ | NM_001362097 | 1258 | 119 | 1037 | scaffold_26 | 35828716 | 31890018 | 31892822 | 3 | 99,57,39, | 119,812,998, | 31890018,31892513,31892783, |
585 | 218 | 27 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001097927 | 1511 | 1166 | 1411 | chrM | 16866 | 2339 | 2584 | 1 | 245, | 1166, | 2339, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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