Schema for Gap - Gap Locations

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Schema for Gap - Gap Locations

Database: dm6 Primary Table: gap Row Count: 572

field	example	SQL type	info
`bin`	748	`smallint(6)`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21485538	`int(10) unsigned`	range
`chromEnd`	21485638	`int(10) unsigned`	range
`ix`	1	`int(11)`	range
`n`	N	`char(1)`	values
`size`	100	`int(10) unsigned`	range
`type`	clone	`varchar(255)`	values
`bridge`	yes	`varchar(255)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	ix	n	size	type	bridge
748	chr2L	21485538	21485638	1	N	100	clone	yes
756	chr2L	22420241	22420341	2	N	100	clone	yes
585	chr2R	4368	4468	3	N	100	clone	yes
585	chr2R	24426	24526	4	N	100	clone	yes
588	chr2R	416884	422884	5	N	6000	clone	yes
590	chr2R	748931	749031	6	N	100	clone	yes
596	chr2R	1472350	1472450	7	N	100	clone	yes
598	chr2R	1826183	1826283	8	N	100	clone	yes
613	chr2R	3759567	3759667	9	N	100	clone	yes
743	chr2R	20780707	20780807	10	N	100	clone	yes

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Gap (gap) Track Description


	Description This track shows the gaps 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 the gaps in this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file. Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap. This assembly contains the following principal types of gaps: other - gaps added at UCSC to annotate strings of Ns that were not marked in the AGP file (count: 572; size range: 10 - 53,860 bases)