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Database: mm8 Primary Table: xenoRefSeqAli Row Count: 193,643   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 | 1192 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 668 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 158 | 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 | 4 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 733 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 6 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 33264 | 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_173526 | varchar(255) | values | Query sequence name |
qSize | 1751 | int(10) unsigned | range | Query sequence size |
qStart | 134 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1693 | int(10) unsigned | range | Alignment end position in query |
tName | chr12 | varchar(255) | values | Target sequence name |
tSize | 120463159 | int(10) unsigned | range | Target sequence size |
tStart | 79617995 | int(10) unsigned | range | Alignment start position in target |
tEnd | 79652085 | int(10) unsigned | range | Alignment end position in target |
blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 48,69,206,274,132,34,63, | longblob | | Size of each block |
qStarts | 134,327,396,602,1183,1473,1... | longblob | | Start of each block in query. |
tStarts | 79617995,79629191,79630897,... | 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)
mm8.all_est.qName (via xenoRefSeqAli.qName)
mm8.all_mrna.qName (via xenoRefSeqAli.qName)
mm8.refGene.name (via xenoRefSeqAli.qName)
mm8.refSeqAli.qName (via xenoRefSeqAli.qName)
mm8.xenoMrna.qName (via xenoRefSeqAli.qName)
mm8.xenoRefFlat.name (via xenoRefSeqAli.qName)
mm8.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 |
---|
1192 | 668 | 158 | 0 | 0 | 4 | 733 | 6 | 33264 | ++ | NM_173526 | 1751 | 134 | 1693 | chr12 | 120463159 | 79617995 | 79652085 | 7 | 48,69,206,274,132,34,63, | 134,327,396,602,1183,1473,1630, | 79617995,79629191,79630897,79633759,79638253,79650988,79652022, |
76 | 3139 | 240 | 0 | 0 | 14 | 318 | 13 | 454555 | +- | NM_001011971 | 3727 | 14 | 3711 | chr1 | 197069962 | 3204560 | 3662494 | 22 | 186,17,54,134,53,76,416,200,1046,82,81,64,24,119,34,45,95,56,106,32,262,197, | 14,200,220,280,415,468,544,960,1160,2217,2316,2400,2479,2740,2871,2905,2951,3050,3108,3214,3248,3514, | 193407468,193407655,193407672,193407733,193407867,193407925,193408914,193657980,193862913,193863959,193864043,193864126,19386420 ... |
76 | 1773 | 173 | 0 | 0 | 3 | 147 | 3 | 453512 | +- | NM_001033036 | 2343 | 60 | 2153 | chr1 | 197069962 | 3206011 | 3661469 | 6 | 179,267,262,200,961,77, | 60,374,644,906,1106,2076, | 193408493,193408801,193409068,193657980,193862913,193863874, |
76 | 1166 | 364 | 0 | 0 | 4 | 309 | 7 | 453797 | +- | NM_001012258 | 2209 | 58 | 1897 | chr1 | 197069962 | 3206102 | 3661429 | 8 | 39,69,243,45,88,195,569,282, | 58,97,241,571,661,749,944,1615, | 193408533,193408575,193408815,193409148,193409247,193657985,193862913,193863578, |
76 | 1386 | 324 | 0 | 0 | 2 | 147 | 6 | 453620 | +- | NM_001032307 | 2993 | 112 | 1969 | chr1 | 197069962 | 3206102 | 3661432 | 7 | 41,85,255,59,123,200,947, | 112,153,344,640,699,822,1022, | 193408530,193408574,193408804,193409124,193409207,193657980,193862913, |
76 | 869 | 296 | 0 | 0 | 5 | 332 | 8 | 454165 | +- | NM_001032714 | 1804 | 38 | 1535 | chr1 | 197069962 | 3206102 | 3661432 | 9 | 42,69,258,34,9,77,202,213,261, | 38,80,231,572,614,656,733,935,1274, | 193408530,193408575,193408810,193409154,193409202,193409253,193657980,193863269,193863599, |
612 | 371 | 106 | 0 | 0 | 3 | 207 | 4 | 318 | +- | NM_001077752 | 966 | 84 | 768 | chr1 | 197069962 | 3660634 | 3661429 | 5 | 39,69,243,45,81, | 84,123,267,597,687, | 193408533,193408575,193408815,193409148,193409247, |
618 | 5982 | 704 | 0 | 0 | 8 | 293 | 15 | 9552 | +- | NM_001195676 | 6991 | 0 | 6979 | chr1 | 197069962 | 4334235 | 4350473 | 18 | 145,46,636,172,11,214,123,813,1222,477,108,257,927,1067,215,160,63,30, | 0,145,191,827,999,1010,1224,1355,2168,3390,3887,4045,4305,5247,6314,6613,6836,6949, | 192719489,192719636,192727044,192727800,192729790,192729807,192730024,192730152,192730968,192732193,192732675,192732809,19273306 ... |
618 | 2702 | 784 | 0 | 0 | 20 | 2832 | 18 | 4740 | +- | NM_173958 | 6318 | 0 | 6318 | chr1 | 197069962 | 4334680 | 4342906 | 23 | 33,384,178,173,308,99,23,4,57,120,73,5,163,33,246,348,78,54,261,84,623,36,103, | 0,48,432,610,853,1335,1443,1467,1482,1545,1936,2010,2018,2209,2971,3255,4215,4296,4476,4770,5197,6132,6215, | 192727056,192727101,192727500,192727798,192729853,192730317,192730416,192730439,192730452,192730509,192730885,192730965,19273097 ... |
618 | 3358 | 881 | 0 | 0 | 19 | 2114 | 20 | 3938 | +- | NM_001280013 | 6461 | 46 | 6399 | chr1 | 197069962 | 4334686 | 4342863 | 22 | 363,179,186,249,105,99,23,66,192,123,96,314,599,69,108,78,57,93,315,738,66,121, | 46,429,608,850,1191,1329,1437,1476,1560,1923,2244,2527,2998,3943,4029,4293,4371,4568,4665,5148,6186,6278, | 192727099,192727500,192727799,192729853,192730185,192730317,192730416,192730452,192730527,192730875,192731190,192731473,19273195 ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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