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

Database: dm6 Primary Table: chainDgriRefSeq2 Row Count: 16,045 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25288	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`qName`	NW_025062489	`varchar(255)`	values
`qSize`	2808958	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	1809522	`int(10) unsigned`	range
`qEnd`	1810135	`int(10) unsigned`	range
`id`	12963	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25288	chr2L	23513712	8664	9283	NW_025062489	2808958	+	1809522	1810135	12963
585	13481	chr2L	23513712	8816	9257	NW_025063692	23286615	-	1981001	1981442	23792
73	784350	chr2L	23513712	11215	152877	NW_025062900	26596763	+	102894	272970	317
585	13536	chr2L	23513712	11819	12325	NW_025063692	23286615	-	23219130	23219648	23717
585	91697	chr2L	23513712	22122	24965	NW_025063692	23286615	-	8274348	8277107	2226
585	717967	chr2L	23513712	26287	101627	NW_025062900	26596763	-	26382337	26466865	346
585	8020	chr2L	23513712	27244	28217	NW_025062900	26596763	+	4070601	4071132	38228
585	10364	chr2L	23513712	75070	75368	NW_025063098	31059138	-	2376991	2377289	29843
585	32698	chr2L	23513712	101013	101627	NW_025062900	26596763	-	26477746	26478587	9949
585	9479	chr2L	23513712	101013	101192	NW_025062900	26596763	-	26469932	26470111	32236

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