Schema for D. ananassae Nanopore Chain/Net - D. ananassae Nanopore Chain/Net

Database: DanaCAF1 Primary Table: netDanaNanopore2 Row Count: 28,617 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	scaffold_3594	`varchar(255)`	values
`tStart`	2	`int(10) unsigned`	range
`tEnd`	463	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	utg000085l	`varchar(255)`	values
`qStart`	120228	`int(10) unsigned`	range
`qEnd`	120690	`int(10) unsigned`	range
`chainId`	1227506	`int(10) unsigned`	range
`ali`	461	`int(10) unsigned`	range
`score`	42780	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	0	`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	scaffold_3594	2	463	+	utg000085l	120228	120690	1227506	461	42780	-1	-1	0	top	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_13679	0	560	-	utg000076l	5803498	5804319	1004334	560	52403	-1	-1	821	top	0	0	-1	-1	-1	-1	0	571
585	1	scaffold_2354	0	561	+	utg000028l	518020	518576	1312971	528	39824	-1	-1	556	top	501	0	-1	-1	-1	-1	490	439
585	1	scaffold_2438	0	624	+	utg000011l	3033120	3033744	887006	624	58683	-1	-1	624	top	203	0	-1	-1	-1	-1	39	39
585	1	scaffold_13730	0	628	+	utg000016l	970525	971153	879676	628	59128	-1	-1	628	top	497	481	-1	-1	-1	-1	0	0
585	1	scaffold_3603	0	642	-	utg000132l	111382	112024	860294	642	60339	-1	-1	642	top	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_11121	0	671	+	utg000153l	170212	170883	824609	671	62725	-1	-1	0	top	70	0	-1	-1	-1	-1	0	0
585	1	scaffold_4299	84	618	+	utg000028l	517939	518479	1266953	523	41383	-1	-1	540	top	437	45	-1	-1	-1	-1	361	342
585	2	scaffold_4299	495	506	+	utg000028l	518367	518367	0	0	0	-1	-1	-1	gap	11	0	-1	-1	-1	-1	11	0
585	1	scaffold_13343	2	683	-	utg000146l	3193388	3194069	831793	678	62222	-1	-1	681	top	0	0	-1	-1	-1	-1	678	681

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

D. ananassae Nanopore Chain/Net (danaNanoporeChainNet) Track Description


	Description Scaffolds from the D. ananassae Nanopore assembly are aligned against the D. ananassae genome assembly (DanaCAF1) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description