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

Database: dm6 Primary Table: chainDeugRefSeq2 Row Count: 28,003 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	67611	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9516	`int(10) unsigned`	range
`qName`	NW_024572115	`varchar(255)`	values
`qSize`	630509	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	31970	`int(10) unsigned`	range
`qEnd`	34667	`int(10) unsigned`	range
`id`	52293	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	67611	chr2L	23513712	7557	9516	NW_024572115	630509	-	31970	34667	52293
585	19434	chr2L	23513712	8722	9282	NW_024572964	8075077	+	7302027	7302587	246922
73	9426549	chr2L	23513712	11214	277315	NW_024573245	1057342	+	16892	302232	89
585	7977	chr2L	23513712	28008	28220	NW_024573245	1057342	+	31592	31807	1038989
585	12205	chr2L	23513712	73409	73719	NW_024573245	1057342	+	70900	71263	485256
585	30259	chr2L	23513712	115694	116357	NW_024573052	3859342	+	732258	732922	144568
585	7865	chr2L	23513712	118605	118887	NW_024573245	1057342	+	121540	121822	1060852
585	11039	chr2L	23513712	118712	119543	NW_024573036	2912658	-	752136	752808	588844
585	10097	chr2L	23513712	118712	126216	NW_024573038	13552899	-	5797278	5798407	698098
585	10970	chr2L	23513712	118717	126236	NW_024573036	2912658	+	1086208	1086952	595954

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