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

Database: dm6 Primary Table: netDbiaRefSeq2 Row Count: 238,653 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`	7557	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_025319364	`varchar(255)`	values
`qStart`	1580869	`int(10) unsigned`	range
`qEnd`	1582924	`int(10) unsigned`	range
`chainId`	40424	`int(10) unsigned`	range
`ali`	1377	`int(10) unsigned`	range
`score`	63353	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1401	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	87	`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	tN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7557	9275	+	NW_025319364	1580869	1582924	40424	1377	63353	-1	-1	1401	top	0	0	87	-1	-1	-1	-1	0	0
585	2	chr2L	8072	8215	+	NW_025319364	1581399	1581830	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8347	8403	+	NW_025319364	1581962	1582063	0	0	0	-1	-1	-1	gap	0	0	58	-1	-1	-1	-1	0	0
585	2	chr2L	8547	8674	+	NW_025319364	1582207	1582329	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11214	22107244	+	NW_025319395	48388	18888934	3	3784549	230270304	-1	-1	102403	top	100	1198511	205011	-1	-1	-1	-1	218542	276335
585	2	chr2L	11375	11385	+	NW_025319395	48551	48551	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11658	11769	+	NW_025319395	48841	48944	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12941	13517	+	NW_025319395	50105	50797	0	0	0	-1	-1	-1	gap	0	57	251	-1	-1	-1	-1	0	0
585	2	chr2L	15721	16327	+	NW_025319395	52997	53287	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16389	17049	+	NW_025319395	53349	55663	0	0	0	-1	-1	-1	gap	0	0	1371	-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