Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DvirCAF1 Primary Table: gold Row Count: 18,382 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	scaffold_0	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	4376	`int(10) unsigned`	range
`ix`	1	`int(11)`	range
`type`	D	`char(1)`	values
`frag`	scaffold_0_1	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	4376	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	scaffold_0	0	4376	1	D	scaffold_0_1	0	4376	+
585	scaffold_1	0	2266	2	D	scaffold_1_1	0	2266	+
585	scaffold_1	2853	4991	4	D	scaffold_1_2	0	2138	+
585	scaffold_10	0	1603	5	D	scaffold_10_1	0	1603	+
585	scaffold_100	0	1452	6	D	scaffold_100_1	0	1452	+
585	scaffold_1000	0	2388	7	D	scaffold_1000_1	0	2388	+
585	scaffold_10000	0	2426	8	D	scaffold_10000_1	0	2426	+
585	scaffold_10001	0	1436	9	D	scaffold_10001_1	0	1436	+
585	scaffold_10001	1981	9183	11	D	scaffold_10001_2	0	7202	+
585	scaffold_10002	0	6050	12	D	scaffold_10002_1	0	6050	+

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. virilis 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).