Table 2.

Reproducibility and robustness of variant callers

	Reproducibility	Robustness	Average number of SNVs
Breseq	90.6	90.6	40.3
SNVer	99.4	97.1	27.7
LoFreq	95.7	96.5	57.5

Results were computed from dengue virus sequencing data for six TSV01 DENV2 replicates (see ‘Materials and Methods’ section). Reproducibility was computed as the percentage of SNVs in the replicate datasets that were seen in another replicate and robustness was computed as the percentage of SNVs in the replicates that were seen in the pooled dataset (obtained by combining the replicates; reproducible SNVs were included in the pooled calls).