Schema for DmojWGS Net - DmojWGS (DmojWGS) Alignment Net

Database: DmojImproved Primary Table: netDmojWGS Row Count: 7,492

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	improved_6498	`varchar(255)`	values
`tStart`	0	`int(10) unsigned`	range
`tEnd`	3406532	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	scaffold_6498	`varchar(255)`	values
`qStart`	0	`int(10) unsigned`	range
`qEnd`	3408170	`int(10) unsigned`	range
`chainId`	9	`int(10) unsigned`	range
`ali`	3064301	`int(10) unsigned`	range
`score`	288055679	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2064	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	324170	`int(11)`	range
`qN`	337895	`int(11)`	range
`tR`	1851295	`int(11)`	range
`qR`	1799075	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	121837	`int(11)`	range
`qTrf`	114082	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
9	1	improved_6498	0	3406532	-	scaffold_6498	0	3408170	9	3064301	288055679	-1	-1	2064	top	324170	337895	1851295	1799075	-1	-1	-1	-1	121837	114082
585	2	improved_6498	9428	9550	-	scaffold_6498	3398620	3398742	0	0	0	-1	-1	-1	gap	122	122	122	122	-1	-1	-1	-1	0	0
585	2	improved_6498	17520	49762	-	scaffold_6498	3358408	3390650	0	0	0	-1	-1	-1	gap	31096	31096	1142	1142	-1	-1	-1	-1	76	76
585	2	improved_6498	65053	69102	-	scaffold_6498	3339068	3343117	0	0	0	-1	-1	-1	gap	4049	4049	0	0	-1	-1	-1	-1	0	0
586	2	improved_6498	151914	152404	-	scaffold_6498	3255766	3256256	0	0	0	-1	-1	-1	gap	490	490	0	0	-1	-1	-1	-1	0	0
586	2	improved_6498	154531	155798	-	scaffold_6498	3252372	3253639	0	0	0	-1	-1	-1	gap	1267	1267	0	0	-1	-1	-1	-1	0	0
586	2	improved_6498	157300	166640	-	scaffold_6498	3241530	3250870	0	0	0	-1	-1	-1	gap	9340	9340	0	0	-1	-1	-1	-1	0	0
586	2	improved_6498	193281	194688	-	scaffold_6498	3213482	3214889	0	0	0	-1	-1	-1	gap	1407	1407	0	0	-1	-1	-1	-1	0	0
586	2	improved_6498	199150	203630	-	scaffold_6498	3204540	3209020	0	0	0	-1	-1	-1	gap	4480	4480	0	0	-1	-1	-1	-1	0	0
587	2	improved_6498	292829	294879	-	scaffold_6498	3113291	3115341	0	0	0	-1	-1	-1	gap	2050	2050	0	0	-1	-1	-1	-1	0	0

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

DmojWGS Net (netDmojWGS) Track Description


	Description Genomic scaffolds from the D. mojavensis Comparative Analysis Freeze 1 (CAF1) assembly were aligned against the improved D. mojavensis assembly produced by the Genomics Education Partnership using LAST with default parameters. The alignments are then chained and netted together using the UCSC whole genome alignment protocol. 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