Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DyakCAF1 Primary Table: gold Row Count: 13,522 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	25744	`int(10) unsigned`	range
`ix`	1499	`int(11)`	range
`type`	D	`char(1)`	values
`frag`	chr2L_1	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	25744	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	chr2L	0	25744	1499	D	chr2L_1	0	25744	+
73	chr2L	26744	186925	1501	D	chr2L_2	0	160181	+
586	chr2L	187925	219066	1503	D	chr2L_3	0	31141	+
73	chr2L	219076	601601	1505	D	chr2L_4	0	382525	+
73	chr2L	601611	713804	1507	D	chr2L_5	0	112193	+
73	chr2L	713814	813630	1509	D	chr2L_6	0	99816	+
591	chr2L	815055	817137	1511	D	chr2L_7	0	2082	+
591	chr2L	817740	819142	1513	D	chr2L_8	0	1402	+
9	chr2L	819172	1342741	1515	D	chr2L_9	0	523569	+
9	chr2L	1342751	2431213	1517	D	chr2L_10	0	1088462	+

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. yakuba 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).