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

Database: DserGB1 Primary Table: chainDm6 Row Count: 17,830 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	30241	`double`	range
`tName`	MTTC01000004	`varchar(255)`	values
`tSize`	40564	`int(10) unsigned`	range
`tStart`	33	`int(10) unsigned`	range
`tEnd`	2714	`int(10) unsigned`	range
`qName`	chr3L	`varchar(255)`	values
`qSize`	28110227	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	16792446	`int(10) unsigned`	range
`qEnd`	16796021	`int(10) unsigned`	range
`id`	4443	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	30241	MTTC01000004	40564	33	2714	chr3L	28110227	+	16792446	16796021	4443
585	48123	MTTC01000009	1175489	90793	102257	chrX	23542271	+	18503110	18505448	2837
585	11939	MTTC01000009	1175489	119182	119466	chr3R	32079331	-	15059708	15060130	11312
73	79376	MTTC01000009	1175489	164697	263867	chr2R	25286936	-	19924198	19935872	1846
586	55020	MTTC01000009	1175489	227506	228646	chrX	23542271	-	19004659	19006524	2517
587	26204	MTTC01000009	1175489	318657	333921	chr2R	25286936	-	20133065	20137931	5107
588	17971	MTTC01000009	1175489	423523	423849	chr2R	25286936	-	16193943	16194249	7398
592	32741	MTTC01000009	1175489	943660	944236	chr2R	25286936	-	18259164	18259952	4144
9	68593949	MTTC01000012	6880660	367	6028688	chr2R	25286936	+	8184820	20274496	2
585	10812	MTTC01000012	6880660	37505	39155	chr3R	32079331	-	6333000	6334149	12439

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. serrata genome assembly (DserGB1) 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