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

Database: dm6 Primary Table: netDeleGB2 Row Count: 215,352

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7555	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	KB458310	`varchar(255)`	values
`qStart`	696399	`int(10) unsigned`	range
`qEnd`	698560	`int(10) unsigned`	range
`chainId`	1596	`int(10) unsigned`	range
`ali`	1418	`int(10) unsigned`	range
`score`	57506	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1401	`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	7555	9283	-	KB458310	696399	698560	1596	1418	57506	-1	-1	1401	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8069	8379	-	KB458310	697306	698010	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11206	17248	-	AFFF02006222	19035	27717	382	4154	242403	-1	-1	0	top	150	1778	-1	-1	-1	-1	0	481
585	2	chr2L	11639	11770	-	AFFF02006222	27166	27287	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12946	13515	-	AFFF02006222	25222	25989	0	0	0	-1	-1	-1	gap	57	335	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16317	-	AFFF02006222	21805	22987	0	0	0	-1	-1	-1	gap	93	199	-1	-1	-1	-1	0	0
585	2	chr2L	16439	17027	-	AFFF02006222	19253	21683	0	0	0	-1	-1	-1	gap	0	1244	-1	-1	-1	-1	0	481
585	1	chr2L	21970	39875	-	AFFF02005312	39	17528	265	14978	758226	-1	-1	0	top	696	166	-1	-1	-1	-1	43	0
585	2	chr2L	24238	24738	-	AFFF02005312	15068	15244	0	0	0	-1	-1	-1	gap	246	0	-1	-1	-1	-1	0	0
585	2	chr2L	25332	25434	-	AFFF02005312	14351	14472	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. 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