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

Database: dm6 Primary Table: netDmirRefSeq1 Row Count: 234,525 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`	8733	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_046673	`varchar(255)`	values
`qStart`	15293472	`int(10) unsigned`	range
`qEnd`	15294021	`int(10) unsigned`	range
`chainId`	434598	`int(10) unsigned`	range
`ali`	549	`int(10) unsigned`	range
`score`	19926	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	549	`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	8733	9282	+	NC_046673	15293472	15294021	434598	549	19926	-1	-1	549	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	117977	+	NC_046677	32367741	32498091	343	42519	2071341	-1	-1	0	top	8407	8437	-1	-1	-1	-1	497	1311
585	2	chr2L	11522	11772	+	NC_046677	32368057	32368471	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12936	13515	+	NC_046677	32369646	32369704	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15725	17048	+	NC_046677	32371924	32373988	0	0	0	-1	-1	-1	gap	93	76	-1	-1	-1	-1	0	0
585	2	chr2L	17141	22113	+	NC_046677	32374081	32377119	0	0	0	-1	-1	-1	gap	0	57	-1	-1	-1	-1	0	0
585	2	chr2L	22944	22988	+	NC_046677	32377958	32378035	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	24217	24734	+	NC_046677	32379265	32379308	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	0
585	2	chr2L	25070	25988	+	NC_046677	32379644	32380816	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26068	26282	+	NC_046677	32380895	32381149	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