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Database: mm10 Primary Table: refSeqAli Row Count: 47,382   Data last updated: 2020-08-17
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 76 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 3205 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 0 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 429 | 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 | 2 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 453383 | 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_001011874 | varchar(255) | values | Query sequence name |
qSize | 3652 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 3634 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 195471971 | int(10) unsigned | range | Target sequence size |
tStart | 3214481 | int(10) unsigned | range | Alignment start position in target |
tEnd | 3671498 | int(10) unsigned | range | Alignment end position in target |
blockCount | 3 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 2487,200,947, | longblob | | Size of each block |
qStarts | 18,2505,2705, | longblob | | Start of each block in query. |
tStarts | 3214481,3421701,3670551, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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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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76 | 3205 | 0 | 429 | 0 | 0 | 0 | 2 | 453383 | - | NM_001011874 | 3652 | 0 | 3634 | chr1 | 195471971 | 3214481 | 3671498 | 3 | 2487,200,947, | 18,2505,2705, | 3214481,3421701,3670551, |
77 | 1705 | 0 | 1342 | 0 | 0 | 0 | 3 | 115349 | - | NM_001195662 | 3047 | 0 | 3047 | chr1 | 195471971 | 4290845 | 4409241 | 4 | 2167,172,636,72, | 0,2167,2339,2975, | 4290845,4351909,4352201,4409169, |
618 | 7013 | 0 | 495 | 0 | 0 | 0 | 3 | 9300 | - | NM_011283 | 7508 | 0 | 7508 | chr1 | 195471971 | 4343506 | 4360314 | 4 | 6585,172,636,115, | 0,6585,6757,7393, | 4343506,4351909,4352201,4360199, |
619 | 3288 | 0 | 0 | 0 | 0 | 0 | 3 | 3139 | - | NM_001289464 | 3288 | 0 | 3288 | chr1 | 195471971 | 4490927 | 4497354 | 4 | 1741,391,92,1064, | 0,1741,2132,2224, | 4490927,4493099,4493771,4496290, |
619 | 3704 | 0 | 0 | 0 | 0 | 0 | 3 | 2723 | - | NM_001289465 | 3704 | 0 | 3704 | chr1 | 195471971 | 4490927 | 4497354 | 4 | 1741,92,807,1064, | 0,1741,1833,2640, | 4490927,4493771,4495135,4496290, |
619 | 2960 | 0 | 0 | 0 | 0 | 0 | 3 | 3467 | - | NM_001289466 | 2960 | 0 | 2960 | chr1 | 195471971 | 4490927 | 4497354 | 4 | 1741,92,63,1064, | 0,1741,1833,1896, | 4490927,4493771,4495135,4496290, |
619 | 2897 | 0 | 0 | 0 | 0 | 0 | 2 | 3530 | - | NM_001289467 | 2897 | 0 | 2897 | chr1 | 195471971 | 4490927 | 4497354 | 3 | 1741,92,1064, | 0,1741,1833, | 4490927,4493771,4496290, |
619 | 4071 | 0 | 0 | 0 | 0 | 0 | 4 | 2356 | - | NM_011441 | 4071 | 0 | 4071 | chr1 | 195471971 | 4490927 | 4497354 | 5 | 1741,367,92,807,1064, | 0,1741,2108,2200,3007, | 4490927,4493099,4493771,4495135,4496290, |
621 | 3286 | 0 | 915 | 0 | 0 | 0 | 4 | 8326 | - | NM_001177658 | 4216 | 0 | 4201 | chr1 | 195471971 | 4773199 | 4785726 | 5 | 3602,124,166,155,154, | 15,3617,3741,3907,4062, | 4773199,4777524,4782567,4783950,4785572, |
621 | 1319 | 0 | 597 | 0 | 0 | 0 | 4 | 10611 | - | NM_025300 | 1931 | 0 | 1916 | chr1 | 195471971 | 4773199 | 4785726 | 5 | 1317,124,166,155,154, | 15,1332,1456,1622,1777, | 4773199,4777524,4782567,4783950,4785572, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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