Schema for Assembly - Assembly from Fragments

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Schema for Assembly - Assembly from Fragments

Database: dm6 Primary Table: gold Row Count: 1,870

field	example	SQL type	info
`bin`	1	`smallint(6)`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	23513712	`int(10) unsigned`	range
`ix`	1	`int(11)`	range
`type`	O	`char(1)`	values
`frag`	AE014134.6	`varchar(255)`	values
`fragStart`	0	`int(10) unsigned`	range
`fragEnd`	23513712	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	type	frag	fragStart	fragEnd	strand
1	chr2L	0	23513712	1	O	AE014134.6	0	23513712	+
1	chr2R	0	25286936	1	O	AE013599.5	0	25286936	+
1	chr3L	0	28110227	1	O	AE014296.5	0	28110227	+
1	chr3R	0	32079331	1	O	AE014297.3	0	32079331	+
9	chr4	0	1348131	1	O	AE014135.4	0	1348131	+
585	chrM	0	19524	1	O	KJ947872.2	0	19524	+
585	chrUn_CP007071v1	0	19956	1	W	CP007071.1	0	19956	+
585	chrUn_CP007072v1	0	44411	1	W	CP007072.1	0	44411	+
585	chrUn_CP007073v1	0	13157	1	W	CP007073.1	0	13157	+
585	chrUn_CP007074v1	0	76224	1	W	CP007074.1	0	76224	+

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 sequences used in the Aug. 2014 D. melanogaster genome assembly. Genome assembly procedures are covered in the NCBI assembly documentation. NCBI also provides specific information about this assembly. The definition of this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file. 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. Component types found in this track (with counts of that type in parentheses): W - whole genome shotgun (1,862) O - other sequence (8)