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

Database: DmirGB2 Primary Table: netDm6 Row Count: 255,342 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	CM001516	`varchar(255)`	values
`tStart`	2035	`int(10) unsigned`	range
`tEnd`	4886	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chr2L	`varchar(255)`	values
`qStart`	15073545	`int(10) unsigned`	range
`qEnd`	15073997	`int(10) unsigned`	range
`chainId`	5298	`int(10) unsigned`	range
`ali`	393	`int(10) unsigned`	range
`score`	18256	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	395	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	10	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	1374	`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	tN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	CM001516	2035	4886	-	chr2L	15073545	15073997	5298	393	18256	-1	-1	395	top	10	1374	0	-1	-1	-1	-1	0	0
585	2	CM001516	2271	4726	-	chr2L	15073705	15073762	0	0	0	-1	-1	-1	gap	10	1374	0	-1	-1	-1	-1	0	0
585	3	CM001516	4526	4726	-	chr2L	15073769	15073969	10019	200	10009	0	7	200	syn	0	0	0	-1	-1	-1	-1	0	0
585	1	CM001516	15217	16791	-	chrX	12029784	12031373	1171	1448	63594	-1	-1	0	top	0	0	0	-1	-1	-1	-1	0	0
585	2	CM001516	15331	15369	-	chrX	12031228	12031259	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	CM001516	15764	15808	-	chrX	12030763	12030833	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	CM001516	16168	16211	-	chrX	12030365	12030401	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
73	1	CM001516	18564	184240	-	chrX	1927808	2064998	148	39702	2134581	-1	-1	224	top	2009	16750	18456	-1	-1	-1	-1	6260	2764
585	2	CM001516	18955	18995	-	chrX	2064601	2064614	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	CM001516	19054	19128	-	chrX	2064490	2064542	0	0	0	-1	-1	-1	gap	0	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. miranda genome assembly (DmirGB2) 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