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

Database: dm6 Primary Table: netDkikGB2 Row Count: 222,492

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7570	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	KB459500	`varchar(255)`	values
`qStart`	10880	`int(10) unsigned`	range
`qEnd`	13005	`int(10) unsigned`	range
`chainId`	3367	`int(10) unsigned`	range
`ali`	811	`int(10) unsigned`	range
`score`	35455	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	821	`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	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7570	9281	+	KB459500	10880	13005	3367	811	35455	-1	-1	821	top	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7779	8679	+	KB459500	11098	12403	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11205	17136	-	AFFH02008258	14323	19815	730	3920	198657	-1	-1	0	top	0	150	0	-1	-1	-1	-1	0	0
585	2	chr2L	11536	11772	-	AFFH02008258	19188	19476	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13500	-	AFFH02008258	17889	18024	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16318	-	AFFH02008258	15170	15625	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16430	17046	-	AFFH02008258	14413	15058	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	22113	634192	+	KB459624	435861	994438	148	130911	6923774	-1	-1	0	top	40	27253	19658	-1	-1	-1	-1	11457	12212
585	2	chr2L	24213	24742	+	KB459624	437970	438040	0	0	0	-1	-1	-1	gap	0	249	0	-1	-1	-1	-1	0	0
73	2	chr2L	25071	210715	+	KB459624	438369	517026	0	0	0	-1	-1	-1	gap	0	9826	3021	-1	-1	-1	-1	913	1612

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