|
|
Database: galGal5 Primary Table: refSeqAli Row Count: 7,730   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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 2549 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 11 | 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 | 14 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 9447 | 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_001031401 | varchar(255) | values | Query sequence name |
qSize | 2586 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 2560 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 196202544 | int(10) unsigned | range | Target sequence size |
tStart | 70096 | int(10) unsigned | range | Alignment start position in target |
tEnd | 82103 | int(10) unsigned | range | Alignment end position in target |
blockCount | 15 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 66,84,74,130,111,55,111,111... | longblob | | Size of each block |
qStarts | 0,66,150,224,354,465,520,63... | longblob | | Start of each block in query. |
tStarts | 70096,72158,73495,73696,746... | longblob | | Start of each block in target. |
|
| |
|
|
Connected Tables and Joining Fields
|
|
Sample Rows
|
|
bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
---|
585 | 2549 | 11 | 0 | 0 | 0 | 0 | 14 | 9447 | + | NM_001031401 | 2586 | 0 | 2560 | chr1 | 196202544 | 70096 | 82103 | 15 | 66,84,74,130,111,55,111,111,56,70,134,108,295,72,1083, | 0,66,150,224,354,465,520,631,742,798,868,1002,1110,1405,1477, | 70096,72158,73495,73696,74690,75384,77030,77275,77676,78225,78505,79158,79638,80581,81020, |
585 | 1040 | 0 | 0 | 0 | 0 | 0 | 7 | 2888 | + | NM_001278112 | 1040 | 0 | 1040 | chr1 | 196202544 | 98770 | 102698 | 8 | 150,30,80,80,112,98,84,406, | 0,150,180,260,340,452,550,634, | 98770,98996,99131,100168,101025,101594,101926,102292, |
587 | 110 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_105579 | 110 | 0 | 110 | chr1 | 196202544 | 292473 | 292583 | 1 | 110, | 0, | 292473, |
587 | 97 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_035090 | 97 | 0 | 97 | chr1 | 196202544 | 317085 | 317182 | 1 | 97, | 0, | 317085, |
588 | 485 | 7 | 0 | 0 | 1 | 10 | 5 | 6302 | - | NM_205325 | 813 | 8 | 510 | chr1 | 196202544 | 456694 | 463488 | 6 | 126,72,110,81,45,58, | 303,429,501,611,692,747, | 456694,458584,458864,460549,463375,463430, |
588 | 3601 | 18 | 0 | 0 | 1 | 1 | 2 | 1267 | + | NM_001031589 | 3637 | 0 | 3620 | chr1 | 196202544 | 463905 | 468791 | 4 | 1239,1406,370,604, | 0,1239,2645,3016, | 463905,466410,467817,468187, |
589 | 84 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_035142 | 84 | 0 | 84 | chr1 | 196202544 | 539154 | 539238 | 1 | 84, | 0, | 539154, |
589 | 2591 | 14 | 0 | 0 | 3 | 15 | 15 | 4104 | - | NM_001031572 | 2636 | 1 | 2621 | chr1 | 196202544 | 645078 | 651787 | 18 | 109,40,28,108,453,109,112,169,183,97,106,138,139,179,197,29,254,155, | 15,124,171,205,315,768,877,989,1158,1341,1438,1544,1682,1821,2000,2197,2226,2480, | 645078,645190,645230,645262,645370,645916,646158,646368,646798,647370,647786,647984,648358,648580,648895,649241,650799,651632, |
590 | 1986 | 10 | 0 | 0 | 1 | 1 | 8 | 11488 | + | NM_001031587 | 1997 | 0 | 1997 | chr1 | 196202544 | 664414 | 677898 | 10 | 17,20,290,184,68,31,237,408,119,622, | 0,18,38,328,512,580,611,848,1256,1375, | 664414,664431,665933,668697,669075,669251,669680,674968,676535,677276, |
591 | 2013 | 7 | 0 | 0 | 1 | 2 | 13 | 44762 | + | NM_001030646 | 2042 | 9 | 2031 | chr1 | 196202544 | 792771 | 839553 | 15 | 31,8,232,115,127,141,159,198,102,158,125,223,100,153,148, | 9,40,48,280,395,522,663,822,1020,1122,1280,1405,1628,1730,1883, | 792771,792803,805410,807746,810033,810735,814857,815543,816769,818480,821667,838927,839151,839251,839405, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|