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Clean reads were aligned to the reference chloroplast genome by BWA to obtain comparison files [67]. Used SAMtools and BCFtools to call the variants from the comparison files [68,69]. SNPs and InDels were filtered using VCFtools [70], setting parameters for deletion rates below 50% and minor allele frequencies above 0.05.
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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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