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Fig. 1 | BMC Genomics

Fig. 1

From: Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

Fig. 1

Genotype concordance across platforms at specific variants relevant to pharmacogenomics. a. Concordance at SNPs in ADME genes. Variants were classified as “rare” if the minor allele was present in five or fewer copies in the sample (corresponding to an allele frequency of about 3%. Concordance rates are split according to the genotype calls on the PRMA, which was considered “truth”—reference concordance is at variants where the PRMA is homozygous reference, and non-reference concordance is for all other sites. b. Concordance in HLA genotypes across platforms. Shown are the concordance rates between sequencing and genotyping array data in imputed HLA genotypes. Concordance is shown for 0.4x and 1x sequencing

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