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

Database: dm6 Primary Table: chainDariRefSeq1 Row Count: 13,571 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25995	`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_017127687	`varchar(255)`	values
`qSize`	26536676	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	5528044	`int(10) unsigned`	range
`qEnd`	5528670	`int(10) unsigned`	range
`id`	8124	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25995	chr2L	23513712	8656	9282	NW_017127687	26536676	+	5528044	5528670	8124
1	14562335	chr2L	23513712	11215	20757638	NW_017127683	27840087	+	2103	27459206	7
585	75337	chr2L	23513712	22123	23876	NW_017127686	2233968	+	779821	783664	1731
585	18309	chr2L	23513712	23920	24965	NW_017128385	2706	+	126	697	12554
585	692810	chr2L	23513712	26291	101651	NW_017127683	27840087	-	27744098	27826691	192
585	8098	chr2L	23513712	75114	75367	NW_017127682	29979347	-	19654568	19654821	35264
585	44071	chr2L	23513712	102541	103767	NW_017127683	27840087	-	16146573	16147748	3889
585	9736	chr2L	23513712	118712	126212	NW_017127684	22052390	-	6662983	6664621	26809
585	29137	chr2L	23513712	123339	126223	NW_017127683	27840087	-	27550897	27552880	6987
585	8895	chr2L	23513712	123727	124932	NW_017127683	27840087	+	13628366	13629452	30244

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