Analysis of missed variants between Illumina ES runs. (a) Distribution of variant fraction and coverage per base for missed SNPs in Illumina exome sequencing experiments. In the four Illumina exome sequencing runs, the variant fraction vs. coverage distribution of SNPs called in one run but not in the other three runs is as expected. The majority of single-run calls cluster in the lower range of variant fraction, below the standard threshold of 0.20-0.25 for reliable heterozygous calls. (b) Classification of filtered-out variants that differed between Illumina exome sequencing runs. Comparison of SNP variants called between exome sequencing runs using the same Illumina sequencing platforms (GAII vs. GAII and HiSeq1 vs. HiSeq2) shows that the most common parameter for differences between sequencing runs is the filtering-out of variants due to strand bias in one run versus another; the second parameter is the low variant ratio and third low quality of the called variants which in many cases is influenced by mis-mapping of reads to different other locations in the genome besides the specific target.