Table 1

Validation calls for Pacific Biosciences and Illumina MiSeq
Pacific Biosciences RS Pacific Biosciences RS Illumina MiSeq Illumina MiSeq
called Poly called Mono called Poly called Mono
Confirmed 37 1 38 0
de novoSNP
Confirmed 1 59 5 55

Number of sites called polymorphic and monomorphic by Pacific Biosciences RS and Illumina MiSeq in the validation experiment. Datasets were sequenced from the same amplicons and were downsampled to 70x average coverage for comparison. Pacific Biosciences shows good accuracy with consistently high percentages in all metrics and making only 2 out 98 wrong calls, while MiSeq shows excellent sensitivity and negative predictive value but lower specificity and positive predictive value and 5 out of 98 wrong calls, all of the same class.

Poly = polymorphic site; Mono = monomorphic site.

Carneiro et al.

Carneiro et al. BMC Genomics 2012 13:375   doi:10.1186/1471-2164-13-375

Open Data