Comparing the two testing benchmarks, Ion Proton contains a total of 1557 somatic SNVs while Illumina MiSeq contains 514 SNV – mixed allele frequency pairs, with 175 unique SNVs. More importantly, Ion Proton benchmark was designed to comprehensively characterize the SNV caller performance on close to sequencing error allele frequencies, thus it is enriched with SNVs of < = 3 % allele frequencies, with 0.5 % as the lowest targeted frequency. Plotting the cumulative percentages of SNV numbers at different allele frequencies (Fig. 1) from the two test benchmarks, it is clear the major components of Ion Proton benchmark SNV allele frequencies are at 0.5 %, 1 %, 2 % to 5 %, followed by continuous frequencies until 46 %, the maximum somatic SNV frequency designed in the dataset. Whereas MiSeq data set includes roughly equal percentages of SNVs at 4 discrete allele frequency levels.
