Figure 3

Sensitivity and specificity to detect rare variants on the MiSeq platform. Four replicates of sample BN1 were run on the GAIIx (two each in lanes 1 and 2) and variant calls made on all four replicates at a resolution threshold of 0.01% (10x lower than a previously reported lower threshold) and a base quality threshold of 30 were considered “true” variants. Two MiSeq BN1 replicate calls were each compared to the set of true variants, and the sensitivity and specificity was averaged across the MiSeq replicates. MiSeq shows 43% loss of sensitivity compared with GAIIx but no significant loss of specificity. When the resolution threshold for the MiSeq calls was increased from 0.01% to 0.1%, the sensitivity decreased as expected.