Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DpseGB3 Primary Table: gold Row Count: 9,385 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	14158	`int(10) unsigned`	range
`ix`	3305	`int(11)`	range
`type`	D	`char(1)`	values
`frag`	CH379058_1	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	14158	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	CH379058	0	14158	3305	D	CH379058_1	0	14158	+
585	CH379058	14208	117962	3307	D	CH379058_2	0	103754	+
73	CH379058	118679	306572	3309	D	CH379058_3	0	187893	+
73	CH379058	306757	506857	3311	D	CH379058_4	0	200100	+
73	CH379058	506858	534395	3313	D	CH379058_5	0	27537	+
589	CH379058	535023	606287	3315	D	CH379058_6	0	71264	+
73	CH379058	606288	825228	3317	D	CH379058_7	0	218940	+
73	CH379058	825229	981405	3319	D	CH379058_8	0	156176	+
592	CH379058	981406	983096	3321	D	CH379058_9	0	1690	+
592	CH379058	983098	1001979	3323	D	CH379058_10	0	18881	+

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. pseudoobscura 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).