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

Database: dm6 Primary Table: chainDmirRefSeq1 Row Count: 37,587 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	17603	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8694	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	NC_046674	`varchar(255)`	values
`qSize`	52279357	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	7388303	`int(10) unsigned`	range
`qEnd`	7388891	`int(10) unsigned`	range
`id`	493783	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	17603	chr2L	23513712	8694	9282	NC_046674	52279357	+	7388303	7388891	493783
585	17075	chr2L	23513712	8694	9282	NC_046674	52279357	+	1863037	1863625	509054
585	19926	chr2L	23513712	8733	9282	NC_046673	25342487	+	15293472	15294021	434598
585	2071341	chr2L	23513712	11214	117977	NC_046677	32539841	+	32367741	32498091	343
585	52939	chr2L	23513712	22113	23219	NC_046677	32539841	+	32364712	32365858	124927
585	9129	chr2L	23513712	27244	28219	NC_046677	32539841	-	6940294	6940822	926009
73	817270	chr2L	23513712	117330	153215	NC_046677	32539841	-	177486	217544	1020
585	10599	chr2L	23513712	118712	119543	NC_046677	32539841	+	32164185	32164866	800569
585	8976	chr2L	23513712	118717	119513	NC_046677	32539841	+	18258120	18258833	944798
585	14788	chr2L	23513712	123726	124926	NC_046677	32539841	-	12763228	12764300	586747

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