Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DperCAF1 Primary Table: gold Row Count: 26,813 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	super_0	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	3918	`int(10) unsigned`	range
`ix`	28394	`int(11)`	range
`type`	D	`char(1)`	values
`frag`	super_0_1	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	3918	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	super_0	0	3918	28394	D	super_0_1	0	3918	+
585	super_0	4018	10405	28396	D	super_0_2	0	6387	+
585	super_0	10505	11943	28398	D	super_0_3	0	1438	+
585	super_0	14592	15809	28400	D	super_0_4	0	1217	+
585	super_0	18922	19817	28402	D	super_0_5	0	895	+
585	super_0	24579	27687	28404	D	super_0_6	0	3108	+
585	super_0	28043	63145	28406	D	super_0_7	0	35102	+
585	super_0	63266	102527	28408	D	super_0_8	0	39261	+
585	super_0	102688	103783	28410	D	super_0_9	0	1095	+
73	super_0	103883	194344	28412	D	super_0_10	0	90461	+

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. persimilis 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).