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

Database: dm6 Primary Table: chainDperRefSeq1 Row Count: 29,086 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19991	`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`	NW_020825324	`varchar(255)`	values
`qSize`	2976574	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	198269	`int(10) unsigned`	range
`qEnd`	198818	`int(10) unsigned`	range
`id`	266115	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19991	chr2L	23513712	8733	9282	NW_020825324	2976574	+	198269	198818	266115
585	16125	chr2L	23513712	8733	9282	NW_020825355	1240727	+	70084	70633	323708
585	9886	chr2L	23513712	8733	9258	NW_020825706	4961753	+	3256260	3256785	485666
585	19991	chr2L	23513712	8733	9282	NW_020825324	2976574	+	194504	195053	266114
585	16088	chr2L	23513712	8734	9282	NW_020825367	694535	+	125454	126002	324279
585	2057814	chr2L	23513712	11214	117968	NW_020825298	15130823	-	14779401	14904915	211
585	48797	chr2L	23513712	22113	23156	NW_020825298	15130823	-	14776550	14777638	103420
585	8938	chr2L	23513712	27244	28217	NW_020825298	15130823	-	5229172	5229698	533294
585	7800	chr2L	23513712	75948	76103	NW_020825298	15130823	-	14851404	14851559	636842
73	812337	chr2L	23513712	117330	153215	NW_020825298	15130823	+	356645	402018	716

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