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

Database: dm6 Primary Table: netDhydGB1 Row Count: 143,130 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9257	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NWQH01000219	`varchar(255)`	values
`qStart`	130806	`int(10) unsigned`	range
`qEnd`	131399	`int(10) unsigned`	range
`chainId`	4424	`int(10) unsigned`	range
`ali`	593	`int(10) unsigned`	range
`score`	24210	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	584	`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`	0	`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	chr2L	8664	9257	-	NWQH01000219	130806	131399	4424	593	24210	-1	-1	584	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	148157	-	NWQH01000238	36	136091	466	16876	726198	-1	-1	0	top	8727	2961	-1	-1	-1	-1	532	1921
585	2	chr2L	11521	11770	-	NWQH01000238	135454	135790	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11949	12077	-	NWQH01000238	135129	135275	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	-	NWQH01000238	134227	134272	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14886	14926	-	NWQH01000238	132819	132870	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15728	17049	-	NWQH01000238	130313	132017	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	42
585	2	chr2L	17140	93472	-	NWQH01000238	117343	130222	0	0	0	-1	-1	-1	gap	7782	65	-1	-1	-1	-1	152	0
585	3	chr2L	22122	24968	-	NWQH01000183	182400	186650	1635	2176	91661	-1	-1	0	nonSyn	249	1010	-1	-1	-1	-1	0	40
585	4	chr2L	22689	22737	-	NWQH01000183	185274	186080	0	0	0	-1	-1	-1	gap	0	49	-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