|
|
Database: speTri2 Primary Table: xenoRefSeqAli Row Count: 446,239   Data last updated: 2020-08-20
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 | 557 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 115 | 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 | 3 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 9229 | 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_001171014 | varchar(255) | values | Query sequence name |
qSize | 1775 | int(10) unsigned | range | Query sequence size |
qStart | 887 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1559 | int(10) unsigned | range | Alignment end position in query |
tName | AGTP01130780 | varchar(255) | values | Target sequence name |
tSize | 61863 | int(10) unsigned | range | Target sequence size |
tStart | 1901 | int(10) unsigned | range | Alignment start position in target |
tEnd | 11802 | int(10) unsigned | range | Alignment end position in target |
blockCount | 4 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 138,85,220,229, | longblob | | Size of each block |
qStarts | 887,1025,1110,1330, | longblob | | Start of each block in query. |
tStarts | 1901,3225,4567,11573, | longblob | | Start of each block in target. |
|
| |
|
|
Connected Tables and Joining Fields
|
|
hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
speTri2.all_est.qName (via xenoRefSeqAli.qName)
speTri2.all_mrna.qName (via xenoRefSeqAli.qName)
speTri2.xenoRefFlat.name (via xenoRefSeqAli.qName)
speTri2.xenoRefGene.name (via xenoRefSeqAli.qName)
| |
|
|
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 | 557 | 115 | 0 | 0 | 0 | 0 | 3 | 9229 | ++ | NM_001171014 | 1775 | 887 | 1559 | AGTP01130780 | 61863 | 1901 | 11802 | 4 | 138,85,220,229, | 887,1025,1110,1330, | 1901,3225,4567,11573, |
585 | 513 | 110 | 0 | 0 | 1 | 12 | 3 | 9241 | ++ | NM_001029867 | 1888 | 902 | 1537 | AGTP01130780 | 61863 | 1902 | 11766 | 4 | 137,85,209,192, | 902,1039,1124,1345, | 1902,3225,4567,11574, |
585 | 506 | 121 | 0 | 0 | 1 | 8 | 3 | 9237 | ++ | NM_172881 | 3358 | 900 | 1535 | AGTP01130780 | 61863 | 1902 | 11766 | 4 | 137,73,226,191, | 900,1045,1118,1344, | 1902,3233,4563,11575, |
585 | 519 | 120 | 0 | 0 | 0 | 0 | 4 | 9229 | ++ | NM_153314 | 1819 | 902 | 1541 | AGTP01130780 | 61863 | 1902 | 11770 | 5 | 137,79,225,2,196, | 902,1039,1118,1343,1345, | 1902,3225,4561,4805,11574, |
585 | 554 | 77 | 0 | 0 | 1 | 34 | 4 | 9263 | ++ | NM_001172141 | 1626 | 882 | 1547 | AGTP01130780 | 61863 | 1902 | 11796 | 5 | 136,5,43,224,223, | 882,1018,1023,1100,1324, | 1902,2129,3229,4563,11573, |
585 | 576 | 89 | 0 | 0 | 0 | 0 | 3 | 9229 | ++ | NM_001172143 | 1631 | 884 | 1549 | AGTP01130780 | 61863 | 1902 | 11796 | 4 | 137,81,223,224, | 884,1021,1102,1325, | 1902,3225,4563,11572, |
673 | 1516 | 222 | 0 | 0 | 11 | 279 | 19 | 40393 | ++ | NM_025264 | 2205 | 1 | 2018 | JH393318 | 12730293 | 11569188 | 11611319 | 20 | 144,136,207,199,78,58,83,72,113,109,160,144,5,14,7,10,66,14,47,72, | 1,145,281,492,691,769,827,911,984,1097,1206,1387,1602,1608,1627,1647,1684,1878,1899,1946, | 11569188,11576823,11578226,11578440,11579594,11581563,11587198,11594214,11594761,11604041,11610313,11610494,11610895,11610902,11 ... |
73 | 1169 | 84 | 0 | 0 | 5 | 215 | 13 | 55232 | ++ | NM_006292 | 1534 | 44 | 1512 | JH393338 | 10015545 | 752612 | 809097 | 15 | 15,102,85,33,78,45,4,64,92,203,240,97,33,34,128, | 44,66,168,318,483,561,606,610,674,766,969,1209,1315,1348,1384, | 752612,752633,759675,764197,771741,771822,771876,775898,786756,805574,807236,808798,808895,808934,808969, |
769 | 619 | 85 | 0 | 0 | 1 | 3 | 1 | 2261 | ++ | NM_001046156 | 1540 | 5 | 712 | JH393281 | 41493964 | 24133196 | 24136161 | 3 | 352,298,54, | 5,357,658, | 24133196,24135809,24136107, |
585 | 490 | 145 | 0 | 0 | 3 | 300 | 3 | 51602 | ++ | NM_133894 | 1894 | 903 | 1838 | AGTP01130780 | 61863 | 1902 | 54139 | 4 | 137,214,236,48, | 903,1120,1341,1790, | 1902,4562,11569,54091, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|