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

Database: dm6 Primary Table: netDmauRefSeq1 Row Count: 178,541 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`	4992	`int(10) unsigned`	range
`tEnd`	23512688	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_046667	`varchar(255)`	values
`qStart`	37733	`int(10) unsigned`	range
`qEnd`	23958893	`int(10) unsigned`	range
`chainId`	2	`int(10) unsigned`	range
`ali`	20377258	`int(10) unsigned`	range
`score`	1688030733	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2313111	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	200	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	2270501	`int(11)`	range
`qR`	2695030	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	328752	`int(11)`	range
`qTrf`	366238	`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	4992	23512688	+	NC_046667	37733	23958893	2	20377258	1688030733	-1	-1	2313111	top	200	2270501	2695030	-1	-1	-1	-1	328752	366238
585	2	chr2L	5200	5216	+	NC_046667	39786	39916	0	0	0	-1	-1	-1	gap	0	0	9	-1	-1	-1	-1	16	0
585	2	chr2L	5458	5492	+	NC_046667	42258	42258	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	6028	9673	+	NC_046667	46053	50313	0	0	0	-1	-1	-1	gap	0	0	1962	-1	-1	-1	-1	0	714
585	3	chr2L	6028	6072	-	NC_046670	28842342	28842386	430992	44	2501	-1	-1	0	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	6553	6680	+	NC_046672	183316	183438	278143	122	5586	-1	-1	122	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	7429	9643	-	NC_046672	19028065	19030638	137657	2134	126239	-1	-1	2116	nonSyn	0	0	0	-1	-1	-1	-1	0	64
585	4	chr2L	7790	7802	-	NC_046672	19030280	19030280	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8074	8089	-	NC_046672	19029648	19030008	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	19
585	4	chr2L	8630	8640	-	NC_046672	19029063	19029063	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