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

. 2022 Sep 27;23:205. doi: 10.1186/s13059-022-02764-1

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

© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 9 — False duplications and their correction in the VGP zebra finch assembly. a The NPNT gene in the VGP zebra finch v1.0 assembly bTaeGut1.0 (first release) has the NPNT-like gene adjacent to it with an assembly gap (AG) and discordant 10X linked reads in this region. In contrast, the trio-based assembly (bTaeGut2.pat.W) had no NPNT-like gene, suggesting a false gene gain in bTaeGut1.0. The false duplication we found in this region was collapsed by purge_dups, and the falsely segmented gene structure was recovered. The VGP assembly v1.7 pipeline with purge_dups conducted before scaffolding prevented this false duplication (Additional file 2: Fig. S12). b Dot plot of alignment showing large ~1.9 Mbp false duplication of chromosome 29 (apricot) in the zebra finch VGP v1.0 pipeline assembly, bTaeGut1.0. c The large ~1.9 Mbp of duplications of chromosome 29 in bTaeGut1.0 were prevented in the trio-based assembly. d The 1.8 Mbp duplication was prevented with purging pre-scaffolding in bTaeGut1.4 using the VGP v1.7 pipeline. The boundaries of the scaffolds are represented as gray dashed lines