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

Database: DbipGB2 Primary Table: chainDm6 Row Count: 18,980 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	27580	`double`	range
`tName`	AFFE02000001	`varchar(255)`	values
`tSize`	474	`int(10) unsigned`	range
`tStart`	44	`int(10) unsigned`	range
`tEnd`	474	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	18390319	`int(10) unsigned`	range
`qEnd`	18390774	`int(10) unsigned`	range
`id`	4434	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	27580	AFFE02000001	474	44	474	chr3R	32079331	+	18390319	18390774	4434
585	7853	AFFE02000001	474	316	474	chr3R	32079331	+	18386939	18387096	17869
585	29781	AFFE02000004	1364	70	1181	chr2R	25286936	+	16448332	16449012	4060
585	8207	AFFE02000095	5139	3237	3375	chrX	23542271	-	4199022	4199160	16898
585	19499	AFFE02000126	10180	9549	10069	chr3L	28110227	+	8402497	8403016	6449
585	8941	AFFE02000166	8498	3967	4205	chr2R	25286936	+	5607674	5607909	15304
585	59897	AFFE02000172	70403	64	1262	chr2R	25286936	-	1380235	1381709	1897
585	606289	AFFE02000172	70403	2107	58817	chrX	23542271	-	3515370	3565927	464
585	11884	AFFE02000172	70403	3882	6292	chr3L	28110227	-	14898583	14899021	11187
585	11298	AFFE02000172	70403	3901	6290	chr2L	23513712	-	8913964	8914859	11834

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. bipectinata genome assembly (DbipGB2) 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