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

Database: dm6 Primary Table: chainDsobRefSeq1 Row Count: 16,103 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19708	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	NC_048530	`varchar(255)`	values
`qSize`	24182865	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	11543533	`int(10) unsigned`	range
`qEnd`	11544082	`int(10) unsigned`	range
`id`	23196	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19708	chr2L	23513712	8733	9282	NC_048530	24182865	-	11543533	11544082	23196
73	5880870	chr2L	23513712	11214	1006176	NC_048534	25941769	+	22772065	23398389	68
585	7621	chr2L	23513712	118605	118854	NC_048534	25941769	+	22887119	22887368	107854
585	8811	chr2L	23513712	118712	119026	NC_048532	23815339	+	7587087	7587345	67191
585	16001	chr2L	23513712	119433	126187	NC_048534	25941769	+	14227821	14232147	28971
585	8519	chr2L	23513712	123339	123613	NC_048534	25941769	+	23400894	23401168	74981
585	14160	chr2L	23513712	123687	124926	NC_048534	25941769	+	7340358	7341447	33014
585	11539	chr2L	23513712	123721	126216	NC_048532	23815339	+	7586287	7588817	41620
585	8203	chr2L	23513712	124464	124750	NC_048534	25941769	+	22880776	22881065	85002
585	17943	chr2L	23513712	124480	124919	NC_048534	25941769	+	23402066	23402505	25663

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