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

Database: dm6 Primary Table: netDnovRefSeq1 Row Count: 150,995 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`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_020824842	`varchar(255)`	values
`qStart`	928917	`int(10) unsigned`	range
`qEnd`	929528	`int(10) unsigned`	range
`chainId`	84615	`int(10) unsigned`	range
`ali`	611	`int(10) unsigned`	range
`score`	26525	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	610	`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	9275	+	NW_020824842	928917	929528	84615	611	26525	-1	-1	610	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	152876	+	NW_020824834	25729	231173	531	19414	788283	-1	-1	0	top	8727	7816	-1	-1	-1	-1	532	44661
585	2	chr2L	11347	11404	+	NW_020824834	25864	25909	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11521	11770	+	NW_020824834	26026	26382	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11973	12078	+	NW_020824834	26585	26708	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12931	13517	+	NW_020824834	27565	27615	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15756	17049	+	NW_020824834	29845	32815	0	0	0	-1	-1	-1	gap	93	353	-1	-1	-1	-1	0	0
585	2	chr2L	17144	93472	+	NW_020824834	32910	48957	0	0	0	-1	-1	-1	gap	7782	786	-1	-1	-1	-1	152	326
585	3	chr2L	22122	24968	+	NW_020824833	1703425	1706863	20279	2187	93876	-1	-1	0	nonSyn	249	87	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	+	NW_020824833	1703995	1704563	0	0	0	-1	-1	-1	gap	0	87	-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