Except for allele frequency composition, sequencing depth is also a crucial factor affecting the performances of the SNV callers, especially at the low-frequency ranges. The average depth for Ion Proton sequencing testing benchmark is about 4000x and about 1500x for MiSeq. In addition, despite the amplicon-based capture assay was applied on benchmark datasets from both technologies, the evenness of the depth across the targeted regions is different. When comparing the depth on known testing benchmark SNV loci of two technologies (Fig. 2), the depth distribution for Ion Proton is skewed while the distribution profile for Illumina MiSeq data displays a bell shape. Further, the average depth at SNV loci from both benchmarks are around 3000x, despite the much higher overall depth for Ion Proton. Thus, we speculate lowered recall for some Ion Proton benchmark SNVs, particularly for the ≤ 1 % ones, the identifiable power of which are more sensitive to the depth and read count number sampling variances.
