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Table 2 Significance testing of variant alleles on H3 influenza mixtures

From: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler

  Assembly-specific error test Allele-specific error test Assembly + Allele tests
Mix-in Major change Negligible Major change Negligible Major change Negligible
Percent Fails Sig. Fails Sig. Fails Sig. Fails Sig. Fails Sig. Fails Sig.
0 % 99.9 % 0.1 % 99.9 % 0.1 % 98.2 % 1.8 % 99.6 % 0.4 % 100 %   99.9 % 0.1 %
0.5 70.2 29.8 99.9 0.1 9.8 90.2 99.7 0.3 70.2 29.8 100 0.0
1 3.5 96.5 99.9 0.1   100 99.6 0.4 3.5 96.5 99.9 0.1
2 0.2 99.8 99.9 0.1   100 99.6 0.4 0.2 99.8 99.9 0.1
5   100 99.9 0.1   100 99.6 0.4   100 99.9 0.1
10   100 99.9 0.1   100 99.6 0.4   100 99.9 0.1
20   100 99.9 0.1   100 99.5 0.5   100 99.9 0.1
25   100 99.9 0.1   100 99.6 0.4   100 100 0.0
50   100 99.9 0.1   100 99.5 0.5   100 99.9 0.1
  1. Negligible allele mixtures meant both unmixed parent viruses had frequencies ≥ 98 % or ≤ 1 % while major allele mixtures were defined as one pre-mixture donor virus having ≥ 98 % frequency and the other ≤ 1 % frequency. Variant negatives (negligible mixtures or 0 % mix-in) are highlighted in yellow while variant positives are in green. Cell data were omitted when counts were zero. The null hypothesis was that variants were produced by sequencer error. All tests were with respect to second-order corrected, one-sided 99.9 % binomial confidence intervals. The percentages of minor variant alleles not distinguishable from sequencer error is marked “fails” for failing to reject the null hypothesis. The percentage of variants rejecting the null hypothesis is marked “sig.” for significant and are candidates for calling single nucleotide variants