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

Database: DbipGB2 Primary Table: netDm6 Row Count: 226,839 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	AFFE02000001	`varchar(255)`	values
`tStart`	44	`int(10) unsigned`	range
`tEnd`	474	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr3R	`varchar(255)`	values
`qStart`	18390319	`int(10) unsigned`	range
`qEnd`	18390774	`int(10) unsigned`	range
`chainId`	4434	`int(10) unsigned`	range
`ali`	428	`int(10) unsigned`	range
`score`	27580	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	455	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	34	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	tNewR	qNewR	tOldR	qOldR	qTrf
585	1	AFFE02000001	44	474	+	chr3R	18390319	18390774	4434	428	27580	-1	-1	455	top	0	-1	-1	-1	-1	34
585	1	AFFE02000004	70	1181	+	chr2R	16448332	16449012	4060	502	29781	-1	-1	507	top	0	-1	-1	-1	-1	0
585	2	AFFE02000004	146	156	+	chr2R	16448408	16448408	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	2	AFFE02000004	185	203	+	chr2R	16448437	16448437	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	2	AFFE02000004	452	1027	+	chr2R	16448692	16448864	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	1	KB462897	4397	5239	-	chrX	16081775	16082753	4719	569	26113	-1	-1	0	top	0	-1	-1	-1	-1	0
585	2	KB462897	4563	4836	-	chrX	16082189	16082584	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	1	KB462899	6908	7295	+	chr4	187991	188375	7320	384	17391	-1	-1	0	top	0	-1	-1	-1	-1	0
585	1	KB462900	8750	9331	-	chrX	22579615	22580178	6800	525	18594	-1	-1	563	top	581	-1	-1	-1	-1	0
585	2	KB462900	8860	8890	-	chrX	22580043	22580067	0	0	0	-1	-1	-1	gap	30	-1	-1	-1	-1	0

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