Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: DmirGB2 Primary Table: gold Row Count: 7,154 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(6)`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	2289	`int(10) unsigned`	range
`ix`	1	`int(11)`	range
`type`	D	`char(1)`	values
`frag`	CM001516_1	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	2289	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
585	CM001516	0	2289	1	D	CM001516_1	0	2289	+
585	CM001516	2299	6709	3	D	CM001516_2	0	4410	+
585	CM001516	6719	8284	5	D	CM001516_3	0	1565	+
585	CM001516	10777	36154	7	D	CM001516_4	0	25377	+
585	CM001516	36164	38185	9	D	CM001516_5	0	2021	+
585	CM001516	39241	98664	11	D	CM001516_6	0	59423	+
73	CM001516	98674	173741	13	D	CM001516_7	0	75067	+
586	CM001516	173751	176884	15	D	CM001516_8	0	3133	+
586	CM001516	177807	220211	17	D	CM001516_9	0	42404	+
586	CM001516	220285	244920	19	D	CM001516_10	0	24635	+

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. miranda 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).