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

Database: dm6 Primary Table: chainDnovRefSeq1 Row Count: 21,697 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	26525	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_020824842	`varchar(255)`	values
`qSize`	1619402	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	928917	`int(10) unsigned`	range
`qEnd`	929528	`int(10) unsigned`	range
`id`	84615	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	26525	chr2L	23513712	8664	9275	NW_020824842	1619402	+	928917	929528	84615
73	788283	chr2L	23513712	11215	152876	NW_020824834	2173719	+	25729	231173	531
585	93876	chr2L	23513712	22122	24968	NW_020824833	2434795	+	1703425	1706863	20279
585	731731	chr2L	23513712	26515	101626	NW_020824834	2173719	-	2042282	2134948	596
585	8740	chr2L	23513712	75075	75368	NW_020824808	5214440	-	4812027	4812320	265692
585	47299	chr2L	23513712	102541	103770	NW_020824787	10715899	+	9322880	9324062	46001
585	8975	chr2L	23513712	118712	126212	NW_020824766	4126161	-	438375	440080	255494
585	7727	chr2L	23513712	118712	119016	NW_020824819	2988450	+	1127342	1127647	348234
585	15193	chr2L	23513712	123223	126237	NW_020824800	5986189	-	432557	436057	146747
585	14007	chr2L	23513712	123338	126171	NW_020824819	2988450	+	1126058	1128080	158513

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