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

Database: dm6 Primary Table: chainDspuRefSeq1 Row Count: 55,647 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	64932	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7555	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NC_050613	`varchar(255)`	values
`qSize`	29674291	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	1718799	`int(10) unsigned`	range
`qEnd`	1720873	`int(10) unsigned`	range
`id`	129048	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	64932	chr2L	23513712	7555	9275	NC_050613	29674291	-	1718799	1720873	129048
585	23495	chr2L	23513712	8727	9282	NC_050612	29495227	-	22977557	22978112	461704
1	312088851	chr2L	23513712	11206	13191980	NC_050610	26214193	-	117276	24772281	2
585	7676	chr2L	23513712	17995	18175	NC_050610	26214193	-	124227	124408	3294552
585	240526	chr2L	23513712	47615	52312	NW_023665611	1753883	+	1480353	1485012	16563
585	238827	chr2L	23513712	47678	52312	NW_023665607	86335	-	69253	73851	16758
585	231616	chr2L	23513712	47678	52312	NW_023665642	743962	+	305761	310238	17597
585	206545	chr2L	23513712	47806	51942	NW_023665704	603483	-	27766	32755	21677
585	218640	chr2L	23513712	48227	56899	NC_050611	22167719	+	16338432	16359137	19472
585	40020	chr2L	23513712	90286	91198	NW_023665598	1169767	-	1168745	1169748	240260

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