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(A) Number of SNPs called by both SNP callers, the CASAVA algorithm and SAMTools, with >99% concordant genotype calls, by chromosome. (B) Distribution of Phred scores in SNPs called in PG17 and PG26 (From SAMTools). (C) Distribution of reads used for SNPs calling in PG17 and PG26 (From CASAVA). The median number of used reads was 36 in PG17 and 43 in PG26.
