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

Database: DmojCAF1 Primary Table: chainDhydGB1 Row Count: 20,083 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	15062	`double`	range
`tName`	scaffold_1008	`varchar(255)`	values
`tSize`	949	`int(10) unsigned`	range
`tStart`	15	`int(10) unsigned`	range
`tEnd`	257	`int(10) unsigned`	range
`qName`	NWQH01000020	`varchar(255)`	values
`qSize`	1140764	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	1008755	`int(10) unsigned`	range
`qEnd`	1008992	`int(10) unsigned`	range
`id`	8548	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	15062	scaffold_1008	949	15	257	NWQH01000020	1140764	-	1008755	1008992	8548
585	56252	scaffold_1020	1249	161	1249	NWQH01000098	438190	-	8941	10150	1668
585	123669	scaffold_1029	2544	0	2353	NWQH01000002	2661136	-	532776	535065	765
585	9636	scaffold_1030	1277	0	119	NWQH01000001	3368585	+	3218650	3218769	16942
585	65535	scaffold_1030	1277	122	1277	NWQH01000117	367702	-	217137	218653	1429
585	16410	scaffold_1031	977	29	948	NWQH01000026	1036302	-	350453	351324	7683
585	14392	scaffold_1037	1158	607	1158	NWQH01000168	246184	+	125379	125561	9048
585	33943	scaffold_105	1251	602	1251	NWQH01000011	1375316	-	979721	980308	3147
585	38942	scaffold_1062	1274	481	1274	NWQH01000169	245010	-	111042	112253	2653
585	59132	scaffold_1063	1022	0	1022	NWQH01000038	868489	+	167813	168881	1570

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