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Database: xenTro10 Primary Table: xenoRefSeqAli Row Count: 170,176   Data last updated: 2021-03-24
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 | 196 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 101 | 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 | 3 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 327 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 3 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 24102 | 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_001078583 | varchar(255) | values | Query sequence name |
qSize | 1122 | int(10) unsigned | range | Query sequence size |
qStart | 204 | int(10) unsigned | range | Alignment start position in query |
qEnd | 828 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 217471166 | int(10) unsigned | range | Target sequence size |
tStart | 53888 | int(10) unsigned | range | Alignment start position in target |
tEnd | 78287 | int(10) unsigned | range | Alignment end position in target |
blockCount | 4 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 111,36,66,84, | longblob | | Size of each block |
qStarts | 204,321,561,744, | longblob | | Start of each block in query. |
tStarts | 53888,55059,62337,78203, | 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)
xenTro10.all_est.qName (via xenoRefSeqAli.qName)
xenTro10.all_mrna.qName (via xenoRefSeqAli.qName)
xenTro10.refGene.name (via xenoRefSeqAli.qName)
xenTro10.refSeqAli.qName (via xenoRefSeqAli.qName)
xenTro10.xenoRefFlat.name (via xenoRefSeqAli.qName)
xenTro10.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 | 196 | 101 | 0 | 0 | 3 | 327 | 3 | 24102 | ++ | NM_001078583 | 1122 | 204 | 828 | chr1 | 217471166 | 53888 | 78287 | 4 | 111,36,66,84, | 204,321,561,744, | 53888,55059,62337,78203, |
585 | 263 | 130 | 0 | 0 | 4 | 549 | 4 | 33352 | ++ | NM_001082696 | 1339 | 238 | 1180 | chr1 | 217471166 | 53888 | 87633 | 5 | 111,36,105,60,81, | 238,355,547,796,1099, | 53888,55059,62286,78215,87552, |
585 | 237 | 108 | 0 | 0 | 3 | 600 | 3 | 33400 | ++ | NM_001285722 | 1161 | 210 | 1155 | chr1 | 217471166 | 53888 | 87633 | 4 | 114,66,72,93, | 210,522,756,1062, | 53888,62289,78203,87540, |
73 | 1602 | 249 | 0 | 24 | 9 | 678 | 11 | 62420 | +- | NM_001092439 | 2610 | 24 | 2577 | chr1 | 217471166 | 130043 | 194338 | 15 | 77,105,192,96,174,289,404,211,89,42,83,49,16,21,27, | 24,101,212,404,500,674,966,1370,1621,1953,2001,2182,2429,2499,2550, | 217276828,217282748,217282853,217283543,217337233,217339001,217339290,217339703,217339960,217340592,217340634,217340758,21734094 ... |
586 | 551 | 97 | 0 | 0 | 1 | 3 | 3 | 3723 | +- | NM_001091176 | 752 | 8 | 659 | chr1 | 217471166 | 200921 | 205292 | 5 | 57,176,147,124,144, | 8,68,244,391,515, | 217265874,217265931,217267553,217269660,217270101, |
587 | 1186 | 413 | 0 | 0 | 5 | 693 | 12 | 59577 | ++ | NM_001145684 | 3362 | 318 | 2610 | chr1 | 217471166 | 263129 | 324305 | 13 | 197,163,27,170,160,39,159,242,114,4,135,112,77, | 318,515,696,1110,1280,1449,1605,1926,2168,2282,2286,2421,2533, | 263129,263593,265371,274812,276003,277895,282114,284401,285972,286198,288415,294496,324228, |
587 | 1124 | 415 | 0 | 0 | 5 | 657 | 11 | 29936 | ++ | NM_001199870 | 2529 | 261 | 2457 | chr1 | 217471166 | 263135 | 294610 | 12 | 191,160,75,174,150,24,156,240,117,3,135,114, | 261,452,726,1032,1206,1495,1530,1848,2088,2205,2208,2343, | 263135,263593,265464,274812,276007,278016,282117,284401,285970,286199,288415,294496, |
587 | 1237 | 440 | 0 | 0 | 6 | 456 | 13 | 59487 | ++ | NM_001107866 | 2840 | 275 | 2408 | chr1 | 217471166 | 263138 | 324302 | 14 | 184,167,33,147,174,24,165,102,242,115,3,139,110,72, | 275,459,632,689,1067,1310,1394,1559,1727,1969,2084,2087,2226,2336, | 263138,263589,265362,265419,274812,276076,277883,282601,284401,285972,286099,288415,294500,324230, |
587 | 1171 | 386 | 0 | 0 | 6 | 573 | 12 | 59607 | ++ | NM_001192969 | 2841 | 222 | 2352 | chr1 | 217471166 | 263138 | 324302 | 13 | 184,167,27,147,174,75,102,242,115,3,135,112,74, | 222,406,585,636,1011,1413,1503,1671,1913,2028,2031,2166,2278, | 263138,263589,265368,265419,274812,282180,282601,284401,285972,286099,288415,294496,324228, |
587 | 1055 | 331 | 0 | 0 | 4 | 318 | 10 | 59784 | ++ | NM_001289164 | 3254 | 208 | 1912 | chr1 | 217471166 | 263138 | 324308 | 11 | 184,164,174,75,102,242,115,3,135,114,78, | 208,392,565,967,1057,1225,1467,1582,1585,1720,1834, | 263138,263589,274812,282180,282601,284401,285972,286099,288415,294496,324230, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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