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Database: mm7 Primary Table: xenoRefSeqAli Row Count: 291,155   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 | info | description |
bin | 824 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 3107 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 665 | 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 | 5 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 485 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 8 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 6683 | 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_002900 | varchar(255) | values | Query sequence name |
qSize | 4290 | int(10) unsigned | range | Query sequence size |
qStart | 1 | int(10) unsigned | range | Alignment start position in query |
qEnd | 4258 | int(10) unsigned | range | Alignment end position in query |
tName | chr14 | varchar(255) | values | Target sequence name |
tSize | 119226840 | int(10) unsigned | range | Target sequence size |
tStart | 31384931 | int(10) unsigned | range | Alignment start position in target |
tEnd | 31395386 | int(10) unsigned | range | Alignment end position in target |
blockCount | 9 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 48,9,1184,305,1528,191,136,... | longblob | | Size of each block |
qStarts | 1,94,114,1343,1648,3176,336... | longblob | | Start of each block in query. |
tStarts | 31384931,31385012,31385029,... | 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)
mm7.all_est.qName (via xenoRefSeqAli.qName)
mm7.all_mrna.qName (via xenoRefSeqAli.qName)
mm7.refGene.name (via xenoRefSeqAli.qName)
mm7.refSeqAli.qName (via xenoRefSeqAli.qName)
mm7.xenoMrna.qName (via xenoRefSeqAli.qName)
mm7.xenoRefFlat.name (via xenoRefSeqAli.qName)
mm7.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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824 | 3107 | 665 | 0 | 0 | 5 | 485 | 8 | 6683 | ++ | NM_002900 | 4290 | 1 | 4258 | chr14 | 119226840 | 31384931 | 31395386 | 9 | 48,9,1184,305,1528,191,136,311,60, | 1,94,114,1343,1648,3176,3367,3504,4198, | 31384931,31385012,31385029,31386252,31386667,31389541,31391602,31393442,31395326, |
825 | 926 | 256 | 0 | 0 | 1 | 88 | 1 | 84 | +- | NM_005972 | 2033 | 481 | 1751 | chr14 | 119226840 | 31578697 | 31579963 | 2 | 1155,27, | 481,1724, | 87646877,87648116, |
826 | 996 | 182 | 0 | 0 | 4 | 82 | 6 | 6012 | ++ | NM_031912 | 5724 | 47 | 1307 | chr14 | 119226840 | 31653610 | 31660800 | 8 | 45,90,141,297,171,121,181,132, | 47,98,245,395,692,863,984,1175, | 31653610,31653655,31654309,31655461,31657526,31658631,31659620,31660668, |
76 | 3121 | 240 | 0 | 0 | 14 | 336 | 14 | 453269 | +- | NM_001011971 | 3727 | 14 | 3711 | chr1 | 194923535 | 3211361 | 3667991 | 21 | 186,17,54,134,53,76,416,200,1046,82,82,63,24,118,34,45,97,52,123,262,197, | 14,200,220,280,415,468,544,960,1160,2217,2316,2401,2479,2740,2871,2905,2951,3054,3108,3248,3514, | 191255544,191255731,191255748,191255809,191255943,191256001,191256990,191506056,191709685,191710731,191710815,191710899,19171097 ... |
76 | 1770 | 171 | 0 | 0 | 3 | 147 | 3 | 452208 | +- | NM_001033036 | 2343 | 60 | 2148 | chr1 | 194923535 | 3212817 | 3666966 | 6 | 179,267,262,200,961,72, | 60,374,644,906,1106,2076, | 191256569,191256877,191257144,191506056,191709685,191710646, |
76 | 1186 | 366 | 0 | 0 | 5 | 360 | 8 | 452527 | +- | NM_001012258 | 2209 | 58 | 1970 | chr1 | 194923535 | 3212847 | 3666926 | 9 | 39,69,244,45,88,195,569,282,21, | 58,97,241,571,661,749,944,1615,1949, | 191256609,191256651,191256891,191257224,191257323,191506061,191709685,191710350,191710667, |
76 | 862 | 299 | 0 | 0 | 4 | 336 | 7 | 452865 | +- | NM_001032714 | 1804 | 38 | 1535 | chr1 | 194923535 | 3212903 | 3666929 | 8 | 42,69,258,39,77,202,213,261, | 38,80,231,566,656,733,935,1274, | 191256606,191256651,191256886,191257224,191257329,191506056,191710041,191710371, |
76 | 1387 | 324 | 0 | 0 | 2 | 147 | 6 | 452316 | +- | NM_001032307 | 2993 | 111 | 1969 | chr1 | 194923535 | 3212903 | 3666930 | 7 | 42,85,255,59,123,200,947, | 111,153,344,640,699,822,1022, | 191256605,191256650,191256880,191257200,191257283,191506056,191709685, |
76 | 495 | 231 | 0 | 0 | 6 | 294 | 6 | 203711 | +- | NM_001092563 | 3904 | 358 | 1378 | chr1 | 194923535 | 3212978 | 3417415 | 8 | 102,93,297,5,11,4,7,207, | 358,502,619,1020,1027,1038,1045,1171, | 191506120,191709693,191709810,191710213,191710218,191710230,191710236,191710350, |
76 | 499 | 257 | 0 | 0 | 3 | 336 | 2 | 203738 | +- | NM_001012253 | 2303 | 278 | 1370 | chr1 | 194923535 | 3212993 | 3417487 | 4 | 174,414,52,116, | 278,494,1199,1254, | 191506048,191709693,191710374,191710426, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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