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

Database: dm6 Primary Table: netDsecRefSeq1 Row Count: 188,628 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`	23475143	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_045949	`varchar(255)`	values
`qStart`	54606	`int(10) unsigned`	range
`qEnd`	24884615	`int(10) unsigned`	range
`chainId`	2	`int(10) unsigned`	range
`ali`	20369738	`int(10) unsigned`	range
`score`	1678548625	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	3241039	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	200	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	2233665	`int(11)`	range
`qR`	3465288	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	328356	`int(11)`	range
`qTrf`	288861	`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	23475143	+	NC_045949	54606	24884615	2	20369738	1678548625	-1	-1	3241039	top	200	2233665	3465288	-1	-1	-1	-1	328356	288861
585	2	chr2L	5204	5216	+	NC_045949	55114	55500	0	0	0	-1	-1	-1	gap	0	0	227	-1	-1	-1	-1	12	386
585	2	chr2L	5458	5492	+	NC_045949	57488	57488	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	6025	6561	+	NC_045949	61183	61183	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	6025	6072	-	NC_045952	30447080	30447127	1135685	47	2460	-1	-1	25	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	6680	9673	+	NC_045949	61297	78374	0	0	0	-1	-1	-1	gap	0	0	7255	-1	-1	-1	-1	0	5711
585	3	chr2L	6709	6858	-	NC_045952	30447102	30447251	312045	148	8080	-1	-1	149	nonSyn	0	0	111	-1	-1	-1	-1	0	0
585	3	chr2L	7502	9643	-	NC_045954	19338586	19341093	138228	2070	123513	-1	-1	2083	nonSyn	0	0	0	-1	-1	-1	-1	0	39
585	4	chr2L	7793	7805	-	NC_045954	19340800	19340800	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8074	8089	-	NC_045954	19340171	19340531	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	19

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