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Database: rheMac3 Primary Table: refSeqAli Row Count: 6,662 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 |
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| bin | 592 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 3851 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 2 | 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 | 0 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 0 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 13 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 52166 | 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_001261471 | varchar(255) | values | Query sequence name |
| qSize | 3969 | int(10) unsigned | range | Query sequence size |
| qStart | 116 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 3969 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 229590362 | int(10) unsigned | range | Target sequence size |
| tStart | 943636 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 999655 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 14 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 1877,99,157,90,102,345,177,... | longblob | | Size of each block |
| qStarts | 0,1877,1976,2133,2223,2325,... | longblob | | Start of each block in query. |
| tStarts | 943636,947587,956768,963016... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
hgFixed.gbSeq.acc (via refSeqAli.qName)
hgFixed.gbWarn.acc (via refSeqAli.qName)
hgFixed.imageClone.acc (via refSeqAli.qName)
hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
knownGeneV39.kgXref.refseq (via refSeqAli.qName)
knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)
rheMac3.all_est.qName (via refSeqAli.qName)
rheMac3.all_mrna.qName (via refSeqAli.qName)
rheMac3.mrnaOrientInfo.name (via refSeqAli.qName)
rheMac3.refFlat.name (via refSeqAli.qName)
rheMac3.refGene.name (via refSeqAli.qName)
rheMac3.xenoMrna.qName (via refSeqAli.qName)
rheMac3.xenoRefGene.name (via refSeqAli.qName)
rheMac3.xenoRefSeqAli.qName (via refSeqAli.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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| 592 | 3851 | 2 | 0 | 0 | 0 | 0 | 13 | 52166 | - | NM_001261471 | 3969 | 116 | 3969 | chr1 | 229590362 | 943636 | 999655 | 14 | 1877,99,157,90,102,345,177,99,144,150,81,152,163,217, | 0,1877,1976,2133,2223,2325,2670,2847,2946,3090,3240,3321,3473,3636, | 943636,947587,956768,963016,963776,966515,972436,973340,973544,977101,977811,988332,992911,999438, |
| 75 | 2073 | 1 | 0 | 0 | 0 | 0 | 7 | 34047 | - | NM_001258174 | 2158 | 84 | 2158 | chr1 | 229590362 | 2615631 | 2651752 | 8 | 1046,196,134,109,77,123,204,185, | 0,1046,1242,1376,1485,1562,1685,1889, | 2615631,2618074,2620744,2624540,2628379,2633621,2647713,2651567, |
| 75 | 1925 | 9 | 123 | 184 | 4 | 40 | 10 | 30558 | + | NM_001266780 | 2435 | 150 | 2431 | chr1 | 229590362 | 2743203 | 2776002 | 13 | 196,155,145,207,215,131,128,120,7,486,147,61,243, | 150,346,501,646,853,1068,1199,1327,1472,1479,1974,2126,2188, | 2743203,2750106,2759245,2761777,2771489,2773130,2773993,2774548,2775055,2775064,2775551,2775698,2775759, |
| 609 | 1378 | 5 | 0 | 0 | 1 | 662 | 4 | 39568 | + | NM_001257684 | 2148 | 94 | 2139 | chr1 | 229590362 | 3177243 | 3218194 | 5 | 112,176,204,454,437, | 94,206,382,1248,1702, | 3177243,3210768,3216522,3217300,3217757, |
| 76 | 3327 | 5 | 17 | 0 | 0 | 0 | 9 | 43087 | - | NM_001258171 | 3465 | 116 | 3465 | chr1 | 229590362 | 3234969 | 3281405 | 10 | 2474,81,138,89,111,56,97,118,141,44, | 0,2474,2555,2693,2782,2893,2949,3046,3164,3305, | 3234969,3238693,3242502,3265538,3267853,3274580,3277611,3278852,3280923,3281361, |
| 617 | 639 | 2 | 0 | 0 | 0 | 0 | 1 | 514 | + | NM_001266806 | 641 | 0 | 641 | chr1 | 229590362 | 4229302 | 4230457 | 2 | 89,552, | 0,89, | 4229302,4229905, |
| 618 | 90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_032444 | 90 | 0 | 90 | chr1 | 229590362 | 4385805 | 4385895 | 1 | 90, | 0, | 4385805, |
| 618 | 83 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_032520 | 83 | 0 | 83 | chr1 | 229590362 | 4386861 | 4386944 | 1 | 83, | 0, | 4386861, |
| 618 | 1326 | 3 | 0 | 0 | 2 | 591 | 10 | 16023 | + | NM_001163080 | 1920 | 0 | 1920 | chr1 | 229590362 | 4398369 | 4415721 | 11 | 118,81,136,78,86,172,172,141,117,94,134, | 0,118,199,581,659,745,917,1089,1230,1347,1786, | 4398369,4399202,4399373,4401335,4401943,4402479,4403517,4404315,4414121,4414612,4415587, |
| 619 | 1972 | 2 | 0 | 0 | 0 | 0 | 2 | 1955 | + | NM_001257474 | 1979 | 5 | 1979 | chr1 | 229590362 | 4537888 | 4541817 | 3 | 248,195,1531, | 5,253,448, | 4537888,4539883,4540286, |
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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