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

Database: DmojCAF1 Primary Table: chainDgriCAF1 Row Count: 19,459 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	11658	`double`	range
`tName`	scaffold_1020	`varchar(255)`	values
`tSize`	1249	`int(10) unsigned`	range
`tStart`	353	`int(10) unsigned`	range
`tEnd`	1249	`int(10) unsigned`	range
`qName`	scaffold_15110	`varchar(255)`	values
`qSize`	24565398	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	23644876	`int(10) unsigned`	range
`qEnd`	23645745	`int(10) unsigned`	range
`id`	13431	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	11658	scaffold_1020	1249	353	1249	scaffold_15110	24565398	-	23644876	23645745	13431
585	25094	scaffold_1029	2544	321	2235	scaffold_15112	5172618	+	4408299	4410133	6580
585	32381	scaffold_1030	1277	122	895	scaffold_14906	14172833	+	648716	649498	4935
585	21719	scaffold_105	1251	606	1199	scaffold_14906	14172833	+	1349615	1350111	7698
585	10483	scaffold_1062	1274	663	839	scaffold_14906	14172833	-	4399691	4399866	14680
585	23745	scaffold_1063	1022	619	1022	scaffold_15110	24565398	+	4548189	4548577	7023
585	11054	scaffold_1066	1223	998	1178	scaffold_14830	6267026	+	4283932	4284094	14039
585	7572	scaffold_1087	1233	512	649	scaffold_15252	17193109	+	10189283	10189432	19953
585	25621	scaffold_1101	1421	954	1409	scaffold_15126	8399593	-	8108513	8108936	6400
585	11544	scaffold_1114	1117	0	1113	scaffold_14906	14172833	-	8488809	8489011	13532

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