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

Database: dm6 Primary Table: chainDguaRefSeq1 Row Count: 15,572 Data last updated: 2022-08-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19996	`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_022995757	`varchar(255)`	values
`qSize`	2181077	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	976895	`int(10) unsigned`	range
`qEnd`	977444	`int(10) unsigned`	range
`id`	40874	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19996	chr2L	23513712	8733	9282	NW_022995757	2181077	-	976895	977444	40874
73	5813012	chr2L	23513712	11214	1006176	NW_022995746	9093651	-	5996822	6601568	74
585	7667	chr2L	23513712	118712	119010	NW_022995744	12801222	+	7011669	7011911	173608
585	16770	chr2L	23513712	119433	126238	NW_022995748	7882174	-	5695361	5699736	50452
585	8329	chr2L	23513712	123339	123632	NW_022995746	9093651	-	6604092	6604385	133445
585	14103	chr2L	23513712	123687	124926	NW_022995752	5385124	-	4501986	4503075	61464
585	9035	chr2L	23513712	124464	124784	NW_022995746	9093651	-	6100075	6100398	109654
585	16915	chr2L	23513712	124480	124875	NW_022995746	9093651	-	6605268	6605663	49994
585	9558	chr2L	23513712	124609	126216	NW_022995744	12801222	+	7011666	7013397	98093
586	32422	chr2L	23513712	132585	133681	NW_022995753	5024747	-	1129223	1133701	19414

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