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

Database: DrhoGB2 Primary Table: chainDm6 Row Count: 44,349 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	30336	`double`	range
`tName`	AFPP02000002	`varchar(255)`	values
`tSize`	1228	`int(10) unsigned`	range
`tStart`	12	`int(10) unsigned`	range
`tEnd`	1212	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	24177676	`int(10) unsigned`	range
`qEnd`	24178546	`int(10) unsigned`	range
`id`	13889	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	30336	AFPP02000002	1228	12	1212	chr3R	32079331	+	24177676	24178546	13889
585	7799	AFPP02000003	15796	9079	9386	chr3R	32079331	+	22373841	22374148	43011
585	39339	AFPP02000009	1102	0	1083	chr3L	28110227	+	5199909	5200851	10587
585	46002	AFPP02000010	1326	26	1326	chr3R	32079331	-	1545066	1546168	8661
585	70125	AFPP02000011	1060	5	1059	chr3L	28110227	+	5207011	5208547	5134
585	43031	AFPP02000012	1065	2	1065	chr3L	28110227	-	22900486	22901299	9467
585	42054	AFPP02000013	1004	0	993	chr3R	32079331	-	1548432	1549229	9753
585	71159	AFPP02000014	1480	398	1477	chr3L	28110227	-	22893462	22894522	5061
585	55003	AFPP02000015	1141	0	1141	chr3L	28110227	+	5221285	5222342	6718
585	106567	AFPP02000016	2403	78	2403	chr3L	28110227	+	3257456	3259469	3542

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. rhopaloa genome assembly (DrhoGB2) 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