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

Database: dm6 Primary Table: netDsecCAF1 Row Count: 119,585 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`	7502	`int(10) unsigned`	range
`tEnd`	9643	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	super_8	`varchar(255)`	values
`qStart`	1391153	`int(10) unsigned`	range
`qEnd`	1393662	`int(10) unsigned`	range
`chainId`	1066	`int(10) unsigned`	range
`ali`	2070	`int(10) unsigned`	range
`score`	122953	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2084	`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`	39	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7502	9643	-	super_8	1391153	1393662	1066	2070	122953	-1	-1	2084	top	0	0	0	-1	-1	-1	-1	0	39
585	2	chr2L	7793	7805	-	super_8	1393369	1393369	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8074	8089	-	super_8	1392739	1393100	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	19
585	2	chr2L	8630	8640	-	super_8	1392155	1392155	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9304	9316	-	super_8	1391484	1391484	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9582	9593	-	super_8	1391203	1391203	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
9	1	chr2L	10011	2138629	+	super_14	18102	2068291	18	1933042	161271509	-1	-1	17552	top	44207	106029	25742	-1	-1	-1	-1	23604	10894
585	2	chr2L	10250	10275	+	super_14	18341	18343	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	10759	10844	+	super_14	18860	18866	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	13129	13471	+	super_14	21192	21504	0	0	0	-1	-1	-1	gap	0	57	295	-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