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

Database: dm6 Primary Table: chainDmojRefSeq2 Row Count: 15,472 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25759	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	NW_025318667	`varchar(255)`	values
`qSize`	31942254	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	5803074	`int(10) unsigned`	range
`qEnd`	5803700	`int(10) unsigned`	range
`id`	35708	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25759	chr2L	23513712	8656	9282	NW_025318667	31942254	+	5803074	5803700	35708
1	16243996	chr2L	23513712	11215	18137931	NW_025318858	24882697	+	66929	22357322	3
585	89722	chr2L	23513712	22123	24965	NW_025318667	31942254	+	31246404	31253782	8757
585	687960	chr2L	23513712	26291	101651	NW_025318858	24882697	-	24723372	24804469	329
585	8222	chr2L	23513712	75114	75367	NW_025318693	11871346	+	6648742	6648995	114475
585	45106	chr2L	23513712	102541	116664	NW_025318858	24882697	-	12209978	12212770	19777
585	9470	chr2L	23513712	118712	126212	NW_025318899	27249912	-	6236814	6239277	94804
585	10413	chr2L	23513712	118718	119513	NW_025318858	24882697	-	2177141	2177855	85606
585	12490	chr2L	23513712	123338	124932	NW_025318858	24882697	+	14748969	14750445	72314
585	28772	chr2L	23513712	123339	126223	NW_025318858	24882697	-	24530496	24532467	31351

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