Schema for Assembly - Assembly from Fragments

Schema for Assembly - Assembly from Fragments

Database: bosTau4 Primary Table: gold Row Count: 131,621
Format description: How to get through chromosome based on fragments

field	example	SQL type	info	description
`bin`	585	`smallint`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	0	`int unsigned`	range	start position in chromosome
`chromEnd`	3267	`int unsigned`	range	end position in chromosome
`ix`	1	`int`	range	ix of this fragment (useless)
`type`	W	`char(1)`	values	(W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
`frag`	AAFC03067444	`varchar(255)`	values	which fragment
`fragStart`	0	`int unsigned`	range	start position in frag
`fragEnd`	3267	`int unsigned`	range	end position in frag
`strand`	-	`char(1)`	values	+ or - (orientation of fragment)

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	chr1	0	3267	1	W	AAFC03067444	0	3267	-
585	chr1	3767	16331	3	W	AAFC03067447	0	12564	+
585	chr1	16331	43834	4	W	AAFC03067448	4	27507	-
585	chr1	43834	123827	5	W	AAFC03067450	27576	107569	+
73	chr1	123827	157105	6	W	AAFC03019678	13741	47019	+
586	chr1	157105	179663	7	W	AAFC03067449	26362	48920	+
586	chr1	179713	194311	9	W	AAFC03019677	0	14598	-
586	chr1	194640	195970	11	W	AAFC03019675	0	1330	+
73	chr1	196020	291673	13	W	AAFC03019679	0	95653	-
587	chr1	291673	296356	14	W	AAFC03125208	0	4683	-

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 cow genome. Whole-genome shotgun reads were assembled into contigs. 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.