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

Database: dm6 Primary Table: chainDsanRefSeq2 Row Count: 60,370 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`score`	539813191	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5244	`int(10) unsigned`	range
`tEnd`	23511661	`int(10) unsigned`	range
`qName`	NC_053016	`varchar(255)`	values
`qSize`	27915280	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	20068	`int(10) unsigned`	range
`qEnd`	27545167	`int(10) unsigned`	range
`id`	4	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
1	539813191	chr2L	23513712	5244	23511661	NC_053016	27915280	+	20068	27545167	4
585	7603	chr2L	23513712	5785	5957	NC_053017	22646313	-	29625	29788	2845062
585	131677	chr2L	23513712	7490	9643	NC_053021	22631256	-	4612133	4614638	49440
585	21271	chr2L	23513712	8733	9282	NC_053018	25621868	+	13054388	13054937	567537
585	10116	chr2L	23513712	11065	11216	NC_053016	27915280	+	24946	25097	1906146
585	9087	chr2L	23513712	16650	16800	NC_053017	22646313	+	457090	457240	2232561
585	10558	chr2L	23513712	16651	16814	NW_025318946	342525	+	223834	223997	1772239
585	10650	chr2L	23513712	16651	16814	NC_053018	25621868	-	9959	10122	1746303
585	8714	chr2L	23513712	19133	19271	NC_053016	27915280	+	29892	30031	2363299
585	9301	chr2L	23513712	19482	19632	NC_053017	22646313	+	457090	457240	2161722

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