Database representation of a net of alignments.
| field | example | SQL type | description |
|---|
| bin | 585 | 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 | 11507 | int(10) unsigned | Start on target |
| tEnd | 38258 | int(10) unsigned | End on target |
| strand | - | char(1) | Orientation of query. + or - |
| qName | GL192379.1 | varchar(255) | Query chromosome |
| qStart | 2832358 | int(10) unsigned | Start on query |
| qEnd | 2862190 | int(10) unsigned | End on query |
| chainId | 3662 | int(10) unsigned | Associated chain Id with alignment details |
| ali | 18754 | int(10) unsigned | Bases in gap-free alignments |
| score | 708002 | 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 | 22178 | 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 | 652 | int(11) | Unsequenced bases on query. -1 for undefined |
| tR | 7322 | int(11) | RepeatMasker bases on target. -1 for undefined |
| qR | 7439 | 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 | 270 | int(11) | Bases of tandem repeats on target. -1 for undefined |
| qTrf | 93 | int(11) | Bases of tandem repeats on query. -1 for undefined |