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. 2019 Nov 15;10:1169. doi: 10.3389/fgene.2019.01169

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Copyright © 2019 Li, Fu, Su, Tian, Du, Zhao, Zheng, Chen, Gao, Cai, Wang, Li and Jiang

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Improvement of reads mapping for resequencing data using pan-genome versus ARS1. (A) Comparison of mapping ratio of resequencing data using pan-genome versus ARS1. (B) The mapping quality of reads from pan-sequences as compared with their original mapping quality on ARS1. (C) The number of identified SNPs for the 10 goat samples using pan-genome versus ARS1. (D) The reads mapping quality was improved within the red rectangle accompanied by repression of false SNPs removal of the low-quality mapped reads. Pan-base specifically refers to the ARS1 proportion in the pan-genome when using the pan-genome as the reference for mapping whereas ARS1 refers to using the ARS1 as the reference for mapping. T-test was used for the comparison. ** P < 0.01.