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Table 2 Specificity of ViVaMBC in plasmid experiment

From: ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

  Pileup ViVaMBC
Mixing prop N ° codons Max noise freq (%) N ° codons Max noise freq (%)
1:200 15,692 1.46 599 0.67
1:100 14,886 1.41 599 0.68
1:50 12,724 1.47 841 0.72
1:10 22,405 1.53 492 0.65
  1. The number of codons in the NS3 are reported after pileup and ViVaMBC. Theoretically, 183(181+2) codons are expected, but far more are reported, especially when piling up the raw data. The maximum frequency of the false positive codons is presented as well. ViVaMBC is able to reduce these frequencies below 1% while they reached more than 1% after Pileup. This illustrated that ViVaMBC is able to reduce drastically the number of false-positive findings and to lower the detection limit above which 100% specificity is expected.