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

Database: dm6 Primary Table: chainDteiRefSeq1 Row Count: 64,457 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`score`	745159934	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5219	`int(10) unsigned`	range
`tEnd`	23512653	`int(10) unsigned`	range
`qName`	NC_053029	`varchar(255)`	values
`qSize`	28277466	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	49946	`int(10) unsigned`	range
`qEnd`	28145161	`int(10) unsigned`	range
`id`	2	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
1	745159934	chr2L	23513712	5219	23512653	NC_053029	28277466	+	49946	28145161	2
585	8945	chr2L	23513712	5768	5957	NC_053030	23768293	-	15135	15448	2217449
585	9748	chr2L	23513712	5772	6708	NC_053030	23768293	-	13628	15249	1960145
585	133639	chr2L	23513712	7497	9642	NC_053034	23880222	+	9213033	9215549	42974
585	20381	chr2L	23513712	8733	9282	NC_053031	24551875	+	12414484	12415033	584318
585	10321	chr2L	23513712	11065	11216	NC_053029	28277466	+	53454	53605	1787696
585	10233	chr2L	23513712	16650	16814	NC_053034	23880222	+	23633253	23633416	1813620
585	10953	chr2L	23513712	19203	19404	NC_053029	28277466	+	58721	58932	1613844
585	26235	chr2L	23513712	19482	60628	NC_053034	23880222	+	23633253	23646566	390798
585	14171	chr2L	23513712	20161	20420	NC_053029	28277466	+	59977	60252	1050806

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