Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DeugGB2 Primary Table: gold Row Count: 7,568

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	AFPQ02000001	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	1356	`int(10) unsigned`	range
`ix`	1	`int(11)`	range
`type`	W	`char(1)`	values
`frag`	AFPQ02000001	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	1356	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	AFPQ02000001	0	1356	1	W	AFPQ02000001	0	1356	+
585	KB464448	0	1775	1	W	AFPQ02000002	0	1775	+
585	KB464448	2839	4493	3	W	AFPQ02000003	0	1654	+
585	AFPQ02000004	0	1047	1	W	AFPQ02000004	0	1047	+
585	AFPQ02000005	0	1025	1	W	AFPQ02000005	0	1025	+
585	AFPQ02000006	0	1030	1	W	AFPQ02000006	0	1030	+
585	AFPQ02000007	0	1132	1	W	AFPQ02000007	0	1132	+
585	AFPQ02000008	0	704	1	W	AFPQ02000008	0	704	+
585	AFPQ02000009	0	1056	1	W	AFPQ02000009	0	1056	+
585	AFPQ02000010	0	1226	1	W	AFPQ02000010	0	1226	+

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

Assembly (gold) Track Description


	Description This track shows the draft assembly of the D. eugracilis genome. Whole-genome shotgun reads were assembled into contigs and when possible, contigs were grouped into scaffolds (also known as "supercontigs"). The order, orientation and gap sizes between contigs within a scaffold are based on paired-end read evidence. In dense mode, this track depicts the contigs that make up the currently-viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks. All components within this track are of fragment type "W" (Whole Genome Shotgun contig).