Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2013 May 8;41(12):e128. doi: 10.1093/nar/gkt339

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 3. — Reconstruction of fosmid-validated duplications. Totally 1000 simulated genomes are constructed and underwent random (A) (discordant) paired-end reads mapped around a validated insertion site chr1:16935160 (from chr1:17069565–17076928 and chr1:16729161–16736531). There are only a few discordant reads that bridge the insertion site to its template (red arrows). Reprever automatically recruits neighboring orphan reads (blue arrows) to increase read coverage for reconstruction. (B) Comparison of reconstructed and true (fosmid) insertion sequences. The reconstructed sequences (Ins.Reprever) are much closer to the true insertions (Ins.fosmid) compared with the template sequences (Ref1 and Ref2). Reconstructed donor sequences at the template sites (Don1, Don2) are almost identical to the templates. (C) Multiple sequence alignment visualization of sequence variation between templates and reconstructed sequences. Highly varied regions including deletions are reconstructed perfectly.

Inline graphic — Reconstruction of fosmid-validated duplications. Totally 1000 simulated genomes are constructed and underwent random (A) (discordant) paired-end reads mapped around a validated insertion site chr1:16935160 (from chr1:17069565–17076928 and chr1:16729161–16736531). There are only a few discordant reads that bridge the insertion site to its template (red arrows). Reprever automatically recruits neighboring orphan reads (blue arrows) to increase read coverage for reconstruction. (B) Comparison of reconstructed and true (fosmid) insertion sequences. The reconstructed sequences (Ins.Reprever) are much closer to the true insertions (Ins.fosmid) compared with the template sequences (Ref1 and Ref2). Reconstructed donor sequences at the template sites (Don1, Don2) are almost identical to the templates. (C) Multiple sequence alignment visualization of sequence variation between templates and reconstructed sequences. Highly varied regions including deletions are reconstructed perfectly.