field | example | SQL type | description |
bin | 608 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
level | 1 | int(10) unsigned | Level of alignment |
tName | chr1 | varchar(255) | Target chromosome |
tStart | 3044216 | int(10) unsigned | Start on target |
tEnd | 3044323 | int(10) unsigned | End on target |
strand | - | char(1) | Orientation of query. + or - |
qName | JH563518 | varchar(255) | Query chromosome |
qStart | 1788321 | int(10) unsigned | Start on query |
qEnd | 1788429 | int(10) unsigned | End on query |
chainId | 5519774 | int(10) unsigned | Associated chain Id with alignment details |
ali | 107 | int(10) unsigned | Bases in gap-free alignments |
score | 3160 | double | Score - a number proportional to 100x matching bases |
qOver | -1 | int(11) | Overlap with parent gap on query side. -1 for undefined |
qFar | -1 | int(11) | Distance from parent gap on query side. -1 for undefined |
qDup | 0 | int(11) | Bases with two or more copies in query. -1 for undefined |
type | top | varchar(255) | Syntenic type: gap/top/syn/nonsyn/inv |
tN | 0 | int(11) | Unsequenced bases on target. -1 for undefined |
qN | 0 | int(11) | Unsequenced bases on query. -1 for undefined |
tR | 0 | int(11) | RepeatMasker bases on target. -1 for undefined |
qR | 0 | int(11) | RepeatMasker bases on query. -1 for undefined |
tNewR | -1 | int(11) | Lineage specific repeats on target. -1 for undefined |
qNewR | -1 | int(11) | Lineage specific repeats on query. -1 for undefined |
tOldR | -1 | int(11) | Bases of ancient repeats on target. -1 for undefined |
qOldR | -1 | int(11) | Bases of ancient repeats on query. -1 for undefined |
tTrf | 0 | int(11) | Bases of tandem repeats on target. -1 for undefined |
qTrf | 0 | int(11) | Bases of tandem repeats on query. -1 for undefined |