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

Database: dm6 Primary Table: chainDyakRefSeq3 Row Count: 60,649 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`score`	542699237	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5244	`int(10) unsigned`	range
`tEnd`	23511915	`int(10) unsigned`	range
`qName`	NC_052527	`varchar(255)`	values
`qSize`	31052931	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	59703	`int(10) unsigned`	range
`qEnd`	29806101	`int(10) unsigned`	range
`id`	4	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
1	542699237	chr2L	23513712	5244	23511915	NC_052527	31052931	+	59703	29806101	4
585	130311	chr2L	23513712	7432	9533	NC_052526	24674056	-	6430711	6433194	48279
585	25600	chr2L	23513712	8733	60628	NC_052529	25180761	+	12966178	12999475	416734
585	9902	chr2L	23513712	11065	11216	NC_052527	31052931	+	62655	62806	2023597
585	10459	chr2L	23513712	16650	16811	NC_052527	31052931	+	29945581	29945742	1844356
585	9079	chr2L	23513712	19134	19271	NC_052527	31052931	+	67599	67736	2298346
585	13339	chr2L	23513712	19482	24335	NC_052527	31052931	+	29945581	29950335	1204962
585	14492	chr2L	23513712	19654	19993	NC_052527	31052931	+	68365	68719	1061000
585	12681	chr2L	23513712	20200	20427	NC_052527	31052931	+	68944	69189	1305476
585	47495	chr2L	23513712	20583	21480	NC_052527	31052931	+	69362	70242	176813

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