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Database: petMar3 Primary Table: all_mrna Row Count: 3,567   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 638 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 647 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 5 | 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 | 4 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 6370 | int(10) unsigned | range | Number of bases inserted in target |
strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | AY130404 | varchar(255) | values | Query sequence name |
qSize | 652 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 652 | int(10) unsigned | range | Alignment end position in query |
tName | PIZI01000001v1 | varchar(255) | values | Target sequence name |
tSize | 27620446 | int(10) unsigned | range | Target sequence size |
tStart | 6957882 | int(10) unsigned | range | Alignment start position in target |
tEnd | 6964904 | int(10) unsigned | range | Alignment end position in target |
blockCount | 5 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 64,167,138,110,173, | longblob | | Size of each block |
qStarts | 0,64,231,369,479, | longblob | | Start of each block in query. |
tStarts | 6957882,6959366,6961998,696... | 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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638 | 647 | 5 | 0 | 0 | 0 | 0 | 4 | 6370 | + | AY130404 | 652 | 0 | 652 | PIZI01000001v1 | 27620446 | 6957882 | 6964904 | 5 | 64,167,138,110,173, | 0,64,231,369,479, | 6957882,6959366,6961998,6963736,6964731, |
655 | 1089 | 12 | 0 | 3 | 20 | 312 | 9 | 1911 | - | KU680735 | 1429 | 13 | 1429 | PIZI01000001v1 | 27620446 | 9191896 | 9194911 | 27 | 7,15,24,84,10,16,16,6,296,55,7,247,19,14,3,13,16,7,9,20,15,15,38,14,43,34,61, | 0,8,24,48,133,144,161,178,185,482,538,545,825,844,859,863,877,893,901,912,932,947,1211,1250,1266,1310,1355, | 9191896,9191903,9191918,9191944,9192028,9192038,9192054,9192070,9192076,9192372,9192427,9192435,9193217,9193237,9193251,9193254, ... |
655 | 59 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | KT235764 | 261 | 197 | 256 | PIZI01000001v1 | 27620446 | 9193885 | 9193944 | 1 | 59, | 197, | 9193885, |
658 | 240 | 0 | 0 | 0 | 0 | 0 | 1 | 105 | + | KU726618 | 240 | 0 | 240 | PIZI01000001v1 | 27620446 | 9603430 | 9603775 | 2 | 73,167, | 0,73, | 9603430,9603608, |
665 | 884 | 1 | 0 | 0 | 0 | 0 | 7 | 6693 | - | KT462564 | 885 | 0 | 885 | PIZI01000001v1 | 27620446 | 10577287 | 10584865 | 8 | 129,135,125,50,122,78,188,58, | 0,129,264,389,439,561,639,827, | 10577287,10578350,10579420,10580206,10580258,10581035,10583599,10584807, |
717 | 1538 | 3 | 0 | 4 | 5 | 18 | 5 | 11274 | - | EU086587 | 1563 | 0 | 1563 | PIZI01000001v1 | 27620446 | 17389421 | 17402240 | 11 | 86,53,90,38,164,734,14,5,108,83,170, | 0,86,142,232,270,434,1169,1195,1200,1309,1393, | 17389421,17389542,17389595,17389686,17392077,17401116,17401850,17401864,17401879,17401987,17402070, |
775 | 4868 | 16 | 0 | 0 | 6 | 14 | 10 | 36486 | + | JN242000 | 4911 | 0 | 4898 | PIZI01000001v1 | 27620446 | 24965772 | 25007142 | 17 | 74,6,62,240,120,160,76,1502,129,1189,212,58,183,33,116,174,550, | 0,74,80,142,382,502,664,740,2242,2371,3561,3773,3836,4020,4053,4172,4348, | 24965772,24965847,24966155,24987082,24993785,24997405,24997565,25001167,25003214,25004622,25005811,25006026,25006084,25006267,25 ... |
612 | 1495 | 0 | 0 | 0 | 2 | 2 | 7 | 34503 | + | EU089674 | 1497 | 0 | 1497 | PIZI01000002v1 | 27533741 | 3539345 | 3575343 | 10 | 48,109,109,84,272,58,235,119,142,319, | 0,48,157,267,352,624,682,917,1036,1178, | 3539345,3558008,3558118,3558227,3558311,3566889,3567586,3570315,3571724,3575024, |
615 | 2039 | 6 | 0 | 0 | 0 | 0 | 4 | 4085 | - | D55629 | 2045 | 0 | 2045 | PIZI01000002v1 | 27533741 | 4016906 | 4023036 | 5 | 1066,164,588,175,52, | 0,1066,1230,1818,1993, | 4016906,4017974,4018140,4020522,4022984, |
84 | 815 | 6 | 0 | 0 | 0 | 0 | 5 | 16055 | + | FJ461777 | 828 | 0 | 821 | PIZI01000002v1 | 27533741 | 11660011 | 11676887 | 6 | 111,96,89,296,106,123, | 0,111,207,296,592,698, | 11660011,11661406,11662590,11673255,11674702,11676764, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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