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

Database: dm6 Primary Table: chainDpseRefSeq1 Row Count: 20,364 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19605	`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_046683	`varchar(255)`	values
`qSize`	68158638	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	9778465	`int(10) unsigned`	range
`qEnd`	9779014	`int(10) unsigned`	range
`id`	110466	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19605	chr2L	23513712	8733	9282	NC_046683	68158638	+	9778465	9779014	110466
585	9672	chr2L	23513712	8733	9258	NC_046679	32422566	+	31450074	31450599	213629
585	16256	chr2L	23513712	8733	9282	NC_046683	68158638	-	7501175	7501724	133681
585	13841	chr2L	23513712	8734	9186	NC_046683	68158638	+	65752383	65752835	154698
585	11280	chr2L	23513712	8874	9188	NC_046679	32422566	-	30639825	30640139	186499
585	8697	chr2L	23513712	8874	9117	NC_046679	32422566	+	1781670	1781913	237527
585	8791	chr2L	23513712	8874	9117	NC_046679	32422566	-	30640299	30640542	234396
585	9386	chr2L	23513712	8908	9188	NC_046679	32422566	+	1781230	1781510	219343
585	2060065	chr2L	23513712	11214	117968	NC_046681	30706867	+	30447320	30573386	183
585	54004	chr2L	23513712	22113	23219	NC_046681	30706867	+	30444274	30445425	32686

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