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

Database: dm6 Primary Table: netDgriCAF1 Row Count: 143,856 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	11215	`int(10) unsigned`	range
`tEnd`	152877	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	scaffold_15252	`varchar(255)`	values
`qStart`	17002063	`int(10) unsigned`	range
`qEnd`	17160374	`int(10) unsigned`	range
`chainId`	217	`int(10) unsigned`	range
`ali`	18416	`int(10) unsigned`	range
`score`	794681	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	0	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	8727	`int(11)`	range
`qR`	6992	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	532	`int(11)`	range
`qTrf`	1544	`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
73	1	chr2L	11215	152877	-	scaffold_15252	17002063	17160374	217	18416	794681	-1	-1	0	top	8727	6992	-1	-1	-1	-1	532	1544
585	2	chr2L	11521	11770	-	scaffold_15252	17159716	17160066	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11923	12077	-	scaffold_15252	17159406	17159563	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13517	-	scaffold_15252	17158492	17158542	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14098	14127	-	scaffold_15252	17157880	17157912	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15718	17050	-	scaffold_15252	17154147	17156300	0	0	0	-1	-1	-1	gap	93	45	-1	-1	-1	-1	0	0
585	2	chr2L	17141	57568	-	scaffold_15252	17089746	17154056	0	0	0	-1	-1	-1	gap	6133	3565	-1	-1	-1	-1	152	797
585	3	chr2L	22122	24965	+	scaffold_15203	11318992	11321751	1234	2234	91697	-1	-1	0	nonSyn	249	130	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	+	scaffold_15203	11319562	11319628	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	23876	23922	+	scaffold_15203	11320764	11321190	0	0	0	-1	-1	-1	gap	0	130	-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. melanogaster genome assembly (dm6) 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