This track indicates any pair of exactly identical sequence for the 26 Nov 2019 Sciurus vulgaris/GCA_902686455.1_mSciVul1.1 genome assembly.
There may be two tracks in this composite collection:
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.
Data in track: Item count: 5; Bases covered: 8,326.
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.
Data in track: Item count: 419,662; Bases covered: 560,751,320.
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.faFiltering 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:
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.
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