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

Database: dm6 Primary Table: netDteiRefSeq1 Row Count: 205,049 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	5219	`int(10) unsigned`	range
`tEnd`	23512653	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_053029	`varchar(255)`	values
`qStart`	49946	`int(10) unsigned`	range
`qEnd`	28145161	`int(10) unsigned`	range
`chainId`	2	`int(10) unsigned`	range
`ali`	10286102	`int(10) unsigned`	range
`score`	745159934	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	3372349	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	200	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	2270310	`int(11)`	range
`qR`	5486388	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	328525	`int(11)`	range
`qTrf`	786843	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
1	1	chr2L	5219	23512653	+	NC_053029	49946	28145161	2	10286102	745159934	-1	-1	3372349	top	200	2270310	5486388	-1	-1	-1	-1	328525	786843
585	2	chr2L	5407	10095	+	NC_053029	50130	52241	0	0	0	-1	-1	-1	gap	0	579	323	-1	-1	-1	-1	0	0
585	3	chr2L	5772	6708	-	NC_053030	23753044	23754665	1960145	251	9748	-1	-1	117	nonSyn	0	160	29	-1	-1	-1	-1	0	0
585	4	chr2L	5906	6588	-	NC_053030	23753161	23754531	0	0	0	-1	-1	-1	gap	0	109	0	-1	-1	-1	-1	0	0
585	5	chr2L	5906	5957	-	NC_053030	23752845	23752896	2217449	51	2440	0	265	0	syn	0	51	51	-1	-1	-1	-1	0	0
585	3	chr2L	7497	9642	+	NC_053034	9213033	9215549	42974	2106	133639	-1	-1	2444	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	9544	9560	+	NC_053034	9215472	9215472	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	10262	10372	+	NC_053029	52407	52684	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	10778	10798	+	NC_053029	53127	53127	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	10931	11214	+	NC_053029	53262	53428	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0

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