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

Database: dm6 Primary Table: netDanaRefSeq2 Row Count: 254,313 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`	8706	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_057932	`varchar(255)`	values
`qStart`	20120448	`int(10) unsigned`	range
`qEnd`	20121023	`int(10) unsigned`	range
`chainId`	282186	`int(10) unsigned`	range
`ali`	575	`int(10) unsigned`	range
`score`	28227	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	575	`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	8706	9281	+	NC_057932	20120448	20121023	282186	575	28227	-1	-1	575	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11263	94386	-	NC_057930	26687679	27001760	891	25043	1081662	-1	-1	286	top	7932	1364	-1	-1	-1	-1	186	12924
585	2	chr2L	11349	11407	-	NC_057930	27001601	27001674	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11523	11772	-	NC_057930	27000524	27001485	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11905	12076	-	NC_057930	27000223	27000391	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	-	NC_057930	26999324	26999371	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17050	-	NC_057930	26995649	26997118	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17136	21958	-	NC_057930	26765262	26995563	0	0	0	-1	-1	-1	gap	0	898	-1	-1	-1	-1	0	11461
585	2	chr2L	22037	22114	-	NC_057930	26765112	26765183	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	22939	22988	-	NC_057930	26764214	26764280	0	0	0	-1	-1	-1	gap	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