Schema for Cat Chain - Cat (Mar. 2006 (Broad/felCat3)) Chained Alignments
Database: hg19
Primary Table: chainFelCat3
Row Count: 1,621,811
Format description: Summary info about a chain of alignments
| field | example | SQL type | description |
| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| score | 757877 | double | score of chain |
| tName | chr1 | varchar(255) | Target sequence name |
| tSize | 249250621 | int(10) unsigned | Target sequence size |
| tStart | 11756 | int(10) unsigned | Alignment start position in target |
| tEnd | 38258 | int(10) unsigned | Alignment end position in target |
| qName | scaffold_212598 | varchar(255) | Query sequence name |
| qSize | 286020 | int(10) unsigned | Query sequence size |
| qStrand | + | char(1) | Query strand |
| qStart | 68566 | int(10) unsigned | Alignment start position in query |
| qEnd | 100790 | int(10) unsigned | Alignment end position in query |
| id | 8684 | int(10) unsigned | chain id |
Connected Tables and Joining Fields
Sample Rows
| bin | score | tName | tSize | tStart | tEnd | qName | qSize | qStrand | qStart | qEnd | id |
|---|
| 585 | 757877 | chr1 | 249250621 | 11756 | 38258 | scaffold_212598 | 286020 | + | 68566 | 100790 | 8684 |
| 585 | 11314 | chr1 | 249250621 | 14414 | 14799 | scaffold_195532 | 201504 | + | 149106 | 149437 | 797680 |
| 585 | 4322 | chr1 | 249250621 | 41160 | 41292 | scaffold_213139 | 77798 | + | 5201 | 5337 | 1484367 |
| 585 | 5085 | chr1 | 249250621 | 41203 | 41350 | scaffold_208471 | 159088 | - | 157805 | 157988 | 1377488 |
| 585 | 10071 | chr1 | 249250621 | 41218 | 41913 | scaffold_185208 | 73300 | - | 46257 | 46870 | 888364 |
| 585 | 11858 | chr1 | 249250621 | 42705 | 43125 | scaffold_75974 | 4234 | + | 0 | 376 | 759174 |
| 585 | 11469 | chr1 | 249250621 | 42797 | 43125 | scaffold_115437 | 35805 | - | 130 | 451 | 786535 |
| 585 | 106998 | chr1 | 249250621 | 47771 | 53725 | scaffold_10731 | 5748 | - | 0 | 3796 | 59700 |
| 585 | 41351 | chr1 | 249250621 | 47990 | 50217 | scaffold_65127 | 1019 | + | 0 | 1013 | 180588 |
| 585 | 34282 | chr1 | 249250621 | 50174 | 51256 | scaffold_52417 | 914 | - | 0 | 913 | 226969 |
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.