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

Database: dm6 Primary Table: chainDkikRefSeq2 Row Count: 27,003 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	38071	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7570	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`qName`	NW_024571405	`varchar(255)`	values
`qSize`	27625346	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	5230443	`int(10) unsigned`	range
`qEnd`	5232568	`int(10) unsigned`	range
`id`	99884	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	38071	chr2L	23513712	7570	9281	NW_024571405	27625346	-	5230443	5232568	99884
585	20370	chr2L	23513712	8679	9273	NW_024571592	21812520	+	9239644	9240244	197810
585	8761	chr2L	23513712	9024	9245	NW_024571435	28719801	+	9336604	9336825	414649
1	102989904	chr2L	23513712	11205	23461797	NW_024571435	28719801	-	13194	28081558	3
585	9929	chr2L	23513712	11210	12419	NW_024571592	21812520	+	15152	15363	373518
585	40455	chr2L	23513712	11210	12474	NW_024571405	27625346	-	12830	14156	93172
585	37669	chr2L	23513712	11210	12934	NW_024571315	33245224	+	17336	18130	101198
585	1447599	chr2L	23513712	25993	102000	NW_024571435	28719801	+	27989558	28698966	403
585	8556	chr2L	23513712	27230	28217	NW_024571435	28719801	-	18277959	18278496	422603
585	7838	chr2L	23513712	28008	28217	NW_024571435	28719801	+	27991683	27991895	458503

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