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

Database: DanaCAF1 Primary Table: netDm6 Row Count: 263,330 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	scaffold_13679	`varchar(255)`	values
`tStart`	0	`int(10) unsigned`	range
`tEnd`	560	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr2R	`varchar(255)`	values
`qStart`	14195000	`int(10) unsigned`	range
`qEnd`	14195560	`int(10) unsigned`	range
`chainId`	2975	`int(10) unsigned`	range
`ali`	560	`int(10) unsigned`	range
`score`	32623	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	129	`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`	541	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	scaffold_13679	0	560	+	chr2R	14195000	14195560	2975	560	32623	-1	-1	129	top	0	0	-1	-1	-1	-1	0	541
585	1	scaffold_3535	448	712	-	chr2L	278024	278288	6286	264	16918	-1	-1	264	top	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_11666	1	754	-	chr3L	2064968	2065721	2081	753	45249	-1	-1	753	top	0	0	-1	-1	-1	-1	753	753
585	1	scaffold_1002	70	705	+	chr2R	4702479	4703282	2459	615	38713	-1	-1	615	top	274	314	-1	-1	-1	-1	0	33
585	2	scaffold_1002	525	539	+	chr2R	4702931	4703119	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	33
585	1	scaffold_2787	224	454	+	chrX	5560172	5560397	10275	220	10769	-1	-1	225	top	112	75	-1	-1	-1	-1	74	71
585	1	scaffold_9258	42	872	+	chr3R	31487683	31488422	2775	560	34843	-1	-1	573	top	0	0	-1	-1	-1	-1	0	2
585	2	scaffold_9258	139	215	+	chr3R	31487780	31487827	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	scaffold_9258	358	412	+	chr3R	31487968	31488009	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	scaffold_9258	513	594	+	chr3R	31488101	31488174	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	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. ananassae genome assembly (DanaCAF1) 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