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Database: danRer4 Primary Table: mgcFullMrna Row Count: 21,531 Data last updated: 2020-01-27
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 | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 760 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 27 | int(10) unsigned | range | Number of bases that don't match |
| repMatches | 54 | 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 | 19 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 5 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 92218 | int(10) unsigned | range | Number of bases inserted in target |
| strand | - | char(2) | values | + or - for strand. First character query, second target (optional) |
| qName | BC095673 | varchar(255) | values | Query sequence name |
| qSize | 1104 | int(10) unsigned | range | Query sequence size |
| qStart | 0 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 860 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 70589895 | int(10) unsigned | range | Target sequence size |
| tStart | 67209 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 160268 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 200,9,4,263,190,76,99, | longblob | | Size of each block |
| qStarts | 244,444,470,475,738,928,1005, | longblob | | Start of each block in query. |
| tStarts | 67209,67410,67445,67449,140... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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danRer4.all_mrna.qName (via mgcFullMrna.qName)
danRer4.mgcGenes.name (via mgcFullMrna.qName)
danRer4.mrnaOrientInfo.name (via mgcFullMrna.qName)
hgFixed.gbCdnaInfo.acc (via mgcFullMrna.qName)
hgFixed.gbSeq.acc (via mgcFullMrna.qName)
hgFixed.imageClone.acc (via mgcFullMrna.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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| 73 | 760 | 27 | 54 | 0 | 3 | 19 | 5 | 92218 | - | BC095673 | 1104 | 0 | 860 | chr1 | 70589895 | 67209 | 160268 | 7 | 200,9,4,263,190,76,99, | 244,444,470,475,738,928,1005, | 67209,67410,67445,67449,140671,160091,160169, |
| 73 | 934 | 0 | 0 | 0 | 0 | 0 | 6 | 27794 | - | BC171362 | 1400 | 466 | 1400 | chr1 | 70589895 | 248001 | 276729 | 7 | 47,53,157,54,255,201,167, | 0,47,100,257,311,566,767, | 248001,256467,260612,261111,271272,275892,276562, |
| 589 | 3227 | 1 | 258 | 0 | 0 | 0 | 21 | 11601 | - | BC162215 | 3486 | 0 | 3486 | chr1 | 70589895 | 576263 | 591350 | 22 | 421,92,102,131,146,124,155,169,151,137,176,193,135,309,269,118,135,114,201,60,114,34, | 0,421,513,615,746,892,1016,1171,1340,1491,1628,1804,1997,2132,2441,2710,2828,2963,3077,3278,3338,3452, | 576263,581925,582111,582354,582591,582812,583023,583253,583513,583741,583959,584223,584526,586099,586489,588542,588746,588969,58 ... |
| 589 | 3226 | 2 | 258 | 0 | 0 | 0 | 21 | 11601 | - | BC162231 | 3486 | 0 | 3486 | chr1 | 70589895 | 576263 | 591350 | 22 | 421,92,102,131,146,124,155,169,151,137,176,193,135,309,269,118,135,114,201,60,114,34, | 0,421,513,615,746,892,1016,1171,1340,1491,1628,1804,1997,2132,2441,2710,2828,2963,3077,3278,3338,3452, | 576263,581925,582111,582354,582591,582812,583023,583253,583513,583741,583959,584223,584526,586099,586489,588542,588746,588969,58 ... |
| 589 | 1623 | 0 | 35 | 0 | 0 | 0 | 3 | 2835 | + | BC068375 | 3511 | 1838 | 3496 | chr1 | 70589895 | 605840 | 610333 | 4 | 55,83,147,1373, | 1838,1893,1976,2123, | 605840,608336,608724,608960, |
| 589 | 1136 | 0 | 66 | 0 | 0 | 0 | 2 | 3052 | + | BC066613 | 1261 | 0 | 1202 | chr1 | 70589895 | 615852 | 620106 | 3 | 42,177,983, | 0,42,219, | 615852,617243,619123, |
| 589 | 1425 | 17 | 148 | 0 | 8 | 501 | 12 | 13181 | - | BC098520 | 2110 | 0 | 2091 | chr1 | 70589895 | 627801 | 642572 | 18 | 78,55,6,30,38,167,112,156,180,258,127,56,125,88,11,29,14,60, | 19,124,179,185,226,267,436,566,724,904,1162,1726,1782,1907,1995,2006,2036,2050, | 627801,628002,628061,628073,628120,628158,628325,628437,628593,628776,632151,633864,634781,636656,637077,637089,637118,642512, |
| 589 | 1830 | 16 | 61 | 0 | 7 | 492 | 13 | 12381 | - | BC125661 | 2662 | 0 | 2399 | chr1 | 70589895 | 628284 | 642572 | 18 | 41,112,156,180,346,30,23,210,75,192,81,109,150,88,11,29,14,60, | 263,306,436,594,774,1120,1160,1205,1415,1490,2119,2200,2309,2459,2547,2558,2588,2602, | 628284,628325,628437,628593,628776,629267,630458,630585,631697,632086,633864,634065,634756,636656,637077,637089,637118,642512, |
| 590 | 958 | 6 | 0 | 0 | 0 | 0 | 8 | 2139 | + | BC164450 | 1348 | 349 | 1313 | chr1 | 70589895 | 676552 | 679655 | 9 | 66,126,82,92,134,106,159,74,125, | 349,415,541,623,715,849,955,1114,1188, | 676552,676723,676982,677137,677433,677701,678306,678853,679530, |
| 590 | 1007 | 8 | 33 | 0 | 1 | 21 | 8 | 2139 | + | BC093351 | 1448 | 359 | 1428 | chr1 | 70589895 | 676552 | 679739 | 10 | 66,126,82,92,134,106,159,74,129,80, | 359,425,551,633,725,859,965,1124,1198,1348, | 676552,676723,676982,677137,677433,677701,678306,678853,679530,679659, |
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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