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

Database: dm6 Primary Table: netDspuRefSeq1 Row Count: 241,498 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7555	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NC_050613	`varchar(255)`	values
`qStart`	27953418	`int(10) unsigned`	range
`qEnd`	27955492	`int(10) unsigned`	range
`chainId`	129048	`int(10) unsigned`	range
`ali`	1388	`int(10) unsigned`	range
`score`	64932	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1405	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7555	9275	-	NC_050613	27953418	27955492	129048	1388	64932	-1	-1	1405	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8072	8218	-	NC_050613	27954492	27954951	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8347	8403	-	NC_050613	27954268	27954363	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8547	8671	-	NC_050613	27954016	27954124	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11206	13191980	-	NC_050610	1441912	26096917	2	4987653	312088851	-1	-1	1991067	top	499041	1008374	-1	-1	-1	-1	142203	500122
585	2	chr2L	11375	11385	-	NC_050610	26096745	26096745	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11753	11764	-	NC_050610	26096356	26096356	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13497	-	NC_050610	26094807	26095187	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16203	-	NC_050610	26092397	26092577	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16410	17049	-	NC_050610	26090797	26092166	0	0	0	-1	-1	-1	gap	0	433	-1	-1	-1	-1	0	25

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