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

Database: dm6 Primary Table: netDbipRefSeq2 Row Count: 255,931 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`	8727	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_025063931	`varchar(255)`	values
`qStart`	6157795	`int(10) unsigned`	range
`qEnd`	6158343	`int(10) unsigned`	range
`chainId`	195499	`int(10) unsigned`	range
`ali`	548	`int(10) unsigned`	range
`score`	26584	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	548	`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	8727	9275	-	NW_025063931	6157795	6158343	195499	548	26584	-1	-1	548	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11263	76079	-	NW_025063924	820076	1117782	1192	19022	795662	-1	-1	1213	top	7856	3250	-1	-1	-1	-1	152	20057
585	2	chr2L	11348	11407	-	NW_025063924	1117625	1117697	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11523	11772	-	NW_025063924	1116578	1117509	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	30
585	2	chr2L	11943	12076	-	NW_025063924	1116277	1116407	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12224	12280	-	NW_025063924	1116084	1116129	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13517	-	NW_025063924	1115386	1115433	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14879	14930	-	NW_025063924	1113973	1114017	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17049	-	NW_025063924	1111627	1113180	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17136	21964	-	NW_025063924	874015	1111540	0	0	0	-1	-1	-1	gap	0	2928	-1	-1	-1	-1	0	18734

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RefSeq Drosophila Chain/Net (refseqDrosChainNet) 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 Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi: 10.1073/pnas.1932072100.

Description