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

Database: dm6 Primary Table: netDariGB1 Row Count: 130,946 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`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	LSRM01000001	`varchar(255)`	values
`qStart`	5528044	`int(10) unsigned`	range
`qEnd`	5528670	`int(10) unsigned`	range
`chainId`	3404	`int(10) unsigned`	range
`ali`	626	`int(10) unsigned`	range
`score`	25995	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	617	`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	8656	9282	+	LSRM01000001	5528044	5528670	3404	626	25995	-1	-1	617	top	0	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	302660	+	LSRM01000002	2103	2485711	24	68657	1567017	-1	-1	7285	top	97667	11912	109669	-1	-1	-1	-1	1130	83302
585	2	chr2L	11521	11770	+	LSRM01000002	2400	2721	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11959	12077	+	LSRM01000002	2910	3046	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12942	13516	+	LSRM01000002	3911	3948	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14890	14934	+	LSRM01000002	5313	5398	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	72
585	2	chr2L	15734	17049	+	LSRM01000002	6198	8026	0	0	0	-1	-1	-1	gap	1	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17140	93472	+	LSRM01000002	8117	21142	0	0	0	-1	-1	-1	gap	0	7782	0	-1	-1	-1	-1	152	0
585	3	chr2L	22123	23876	+	LSRM01000006	779821	783664	1050	1721	75337	-1	-1	0	nonSyn	101	0	1502	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22721	+	LSRM01000006	780390	782502	0	0	0	-1	-1	-1	gap	101	0	1502	-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