Output and downstream analysis modules of AccuSNV. The core outputs include (1) a compressed SNV table in NumPy's NPZ format storing detailed feature vectors and prediction scores; (2) a human-readable text summary file (TSV) listing all identified SNVs with key attributes; (3) a set of quality control (QC) figures summarizing read coverage, base calls, mapping quality scores, etc.; and (4) a HTML report that integrates summary tables and bar charts of identified variants. Homoplasic SNVs in the figure refers to variants in which the same derived nucleotide arises independently in two or more lineages since their divergence from a common ancestor with a different ancestral base. These SNVs can be used to infer parallel, convergent, or revertant evolutionary events (Edwards et al. 2021).