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

Database: dm6 Primary Table: netDhydRefSeq1 Row Count: 138,424 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`	8664	`int(10) unsigned`	range
`tEnd`	9257	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_022045714	`varchar(255)`	values
`qStart`	724815	`int(10) unsigned`	range
`qEnd`	725408	`int(10) unsigned`	range
`chainId`	73931	`int(10) unsigned`	range
`ali`	593	`int(10) unsigned`	range
`score`	24341	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	584	`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	8664	9257	+	NW_022045714	724815	725408	73931	593	24341	-1	-1	584	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	302504	+	NW_022045682	25648	2512782	83	70490	2585969	-1	-1	4898	top	11912	123748	-1	-1	-1	-1	1130	124587
585	2	chr2L	11521	11770	+	NW_022045682	25949	26285	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11949	12077	+	NW_022045682	26464	26610	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	+	NW_022045682	27467	27512	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14886	14926	+	NW_022045682	28869	28920	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15728	17049	+	NW_022045682	29722	31424	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	42
585	2	chr2L	17140	93472	+	NW_022045682	31515	44396	0	0	0	-1	-1	-1	gap	7782	65	-1	-1	-1	-1	152	0
585	3	chr2L	22122	24968	-	NW_022045721	567893	572135	17922	2176	91541	-1	-1	0	nonSyn	249	396	-1	-1	-1	-1	0	32
585	4	chr2L	22689	22737	-	NW_022045721	570759	571565	0	0	0	-1	-1	-1	gap	0	43	-1	-1	-1	-1	0	0

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