Schema for Drosophila Chain/Net - Drosophila Genomes, Chain and Net Alignments

Database: DmojCAF1 Primary Table: chainDnavGB1 Row Count: 29,914 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	39488	`double`	range
`tName`	scaffold_100	`varchar(255)`	values
`tSize`	1892	`int(10) unsigned`	range
`tStart`	0	`int(10) unsigned`	range
`tEnd`	639	`int(10) unsigned`	range
`qName`	LSRL01002063	`varchar(255)`	values
`qSize`	3262	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	1001	`int(10) unsigned`	range
`qEnd`	1640	`int(10) unsigned`	range
`id`	8267	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	39488	scaffold_100	1892	0	639	LSRL01002063	3262	-	1001	1640	8267
585	9873	scaffold_100	1892	397	554	LSRL01005096	1332	-	587	747	24372
585	22183	scaffold_1008	949	0	281	LSRL01003391	1866	-	1555	1852	11904
585	16338	scaffold_1008	949	82	281	LSRL01007137	1129	-	0	214	14971
585	80960	scaffold_1020	1249	22	1249	LSRL01000004	21835025	+	1475918	1477196	4299
585	161510	scaffold_1029	2544	0	2337	LSRL01000003	22154029	-	2817140	2819447	1552
585	17013	scaffold_103	1823	1571	1800	LSRL01000003	22154029	+	9350570	9350798	14517
585	11509	scaffold_1030	1277	0	131	LSRL01000003	22154029	+	7716243	7716374	20545
585	77098	scaffold_1030	1277	122	1277	LSRL01000005	24697304	+	13630554	13631608	4605
585	37734	scaffold_1037	1158	607	1158	LSRL01000003	22154029	+	6731562	6732102	8504

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Drosophila Chain/Net (drosophilaChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. mojavensis genome assembly (DmojCAF1) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description