Schema for Tandem Dups - Paired identical sequences

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Database: mm39 Primary Table: tandemDups Row Count: 858,983 Data last updated: 2020-07-30
Format description: Browser extensible data
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	608	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`chromStart`	3069940	`int(10) unsigned`	Start position in chromosome
`chromEnd`	3087936	`int(10) unsigned`	End position in chromosome
`name`	chr1:3069941-3087936	`varchar(255)`	Name of item
`score`	32	`int(10) unsigned`	Optional score, nominal range 0-1000
`strand`	+	`char(1)`	+ or -
`thickStart`	3069940	`int(10) unsigned`	Start of where display should be thick (start codon)
`thickEnd`	3087936	`int(10) unsigned`	End of where display should be thick (stop codon)
`reserved`	0	`int(10) unsigned`	Used as itemRgb as of 2004-11-22
`blockCount`	2	`int(10) unsigned`	Number of blocks
`blockSizes`	32,32	`longblob`	Comma separated list of block sizes
`chromStarts`	0,17964	`longblob`	Start positions relative to chromStart

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
608	chr1	3069940	3087936	chr1:3069941-3087936	32	+	3069940	3087936	2	32,32	0,17964
608	chr1	3070516	3088497	chr1:3070517-3088497	36	+	3070516	3088497	2	36,36	0,17945
608	chr1	3071680	3089674	chr1:3071681-3089674	38	+	3071680	3089674	2	38,38	0,17956
608	chr1	3082164	3084245	chr1:3082165-3084245	30	+	3082164	3084245	2	30,30	0,2051
608	chr1	3086965	3103121	chr1:3086966-3103121	36	+	3086965	3103121	2	36,36	0,16120
608	chr1	3087373	3103490	chr1:3087374-3103490	30	+	3087373	3103490	2	30,30	0,16087
608	chr1	3087590	3103707	chr1:3087591-3103707	30	+	3087590	3103707	2	30,30	0,16087
608	chr1	3089260	3105366	chr1:3089261-3105366	33	+	3089260	3105366	2	33,33	0,16073
608	chr1	3092614	3109860	chr1:3092615-3109860	34	+	3092614	3109860	2	34,34	0,17212
608	chr1	3092726	3109971	chr1:3092727-3109971	33	+	3092726	3109971	2	33,33	0,17212

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

Tandem Dups (tanDups) Track Description


	Description There are two tracks in this composite collection: Gap Overlaps - Paired exactly identical sequence on each side of a gap Tandem Dups - Paired exactly identical sequence survey over entire genome assembly The Gap Overlaps is thus a subset of the full Tandem Dups track. This investigation began when an unusual number of paired sequences around gaps was noticed during the mouse strain sequencing project. This naturally raised the question, how common is this feature, and what type of assemblies can it be found in. The Gap Overlaps track indicates any pair of exactly identical sequence on each side of gaps. Where a gap is any run of N's, including a single N. The end of an upstream sequence before the gap is duplicated exactly at the beginning of the downstream sequence following the gap in the assembly. The Tandem Dups track is a similar survey over the entire genome assembly. The separation gap between these paired sequences can range from 1 base up to 20,000 bases. Methods The Gap Overlap duplicate sequences were found by extracting 1,000 bases before and after each gap and aligned to each other with the blat command: blat -q=dna -minIdentity=95 -repMatch=10 upstreamContig.fa downstreamContig.fa Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence, and begins exactly at the start of the downstream sequence. The Tandem Dups paired sequences were found with the following procedure: Generate 29 base kmers for the entire genome, allow only kmers with bases: A C T G, no N's allowed. Pair up identical kmers with at least one base separation and up to 20,000 bases separation. Collapse overlapping kmer pairs when they are the same size of sequence and the same spacing between the pairs. This procedure preserves the definition of duplicated identical pairs. The resulting pairs can now be longer sequences with smaller separation then the constituent pairs Final result selects sizes of 30 bases or more for the size of the paired sequence, and at least one base remaining as a separation gap. Collapsed pairs that close the gap are discarded. They appear to indicate simple repeat sequences when this happens. It would be interesting to have this result available, but that is not available at this time. The reason for starting with 29 base sized pairs and then selecting results of at least 30 base sized pairs results in a reasonable number of 30 base pairs. If the procedure starts with 30 base sized pairs, it produces way too many 30 base kmer pairs for a reasonable count. See Also Interactive tables of all results: Gap Overlaps Tandem Dups Credits Thank you to Joel Armstrong and Benedict Paten of the Computational Genomics Lab at the U.C. Santa Cruz Genomics Institute for identifying this characteristic of genome assemblies. The data and presentation of this track were prepared by Hiram Clawson, U.C. Santa Cruz Genomics Institute

Description

Methods

See Also

Credits