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

Database: dm6 Primary Table: chainDeleRefSeq2 Row Count: 25,557 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	56670	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7555	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`qName`	NW_024545513	`varchar(255)`	values
`qSize`	26751529	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	3017473	`int(10) unsigned`	range
`qEnd`	3019634	`int(10) unsigned`	range
`id`	55941	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	56670	chr2L	23513712	7555	9283	NW_024545513	26751529	-	3017473	3019634	55941
585	23577	chr2L	23513712	8732	9282	NW_024545578	28425668	+	8623179	8623729	162630
585	241839	chr2L	23513712	11206	17248	NW_024545730	88819	+	5176	13860	5338
585	757280	chr2L	23513712	21970	39875	NW_024546167	21933072	+	21915439	21932924	829
585	7821	chr2L	23513712	28008	28218	NW_024546167	21933072	+	21921392	21921605	506871
585	8069	chr2L	23513712	28404	28642	NW_024546167	21933072	+	21921003	21921238	489549
585	1601175	chr2L	23513712	40374	102038	NW_024545730	88819	-	1404	72089	196
585	281891	chr2L	23513712	47600	52327	NW_024546167	21933072	-	12205025	12209711	4065
585	274797	chr2L	23513712	47600	52327	NW_024546078	426726	-	229480	234126	4261
585	281769	chr2L	23513712	47600	52327	NW_024545513	26751529	+	15377772	15382458	4071

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