Graphs Built From Reported Results

 Quick Analysis Plan Copied

 Long Analysis Plan

Evidence-Backed Graphing Plan: SARS-CoV-2 Mutation Effect Sizes

Only mutations with reported quantitative or clearly directional effects from the supplied sources should be graphed. The defensible set is: D614G spike (higher infectious titers in pseudovirus assays, enhanced replication in human airway tissues and hamster upper respiratory tracts) D614G fitness Nature study; nsp1 Δ82-85 and Δ83-86 (significantly reduced interferon-signaling inhibition, no virulence effect in hamsters) nsp1 mutation immune modulation study; mutation rates (SARS-CoV-2 1.3×10⁻⁶±0.2×10⁻⁶, Influenza 2.0×10⁻⁶±0.6×10⁻⁶, Rhinovirus 3.4×10⁻⁴ per base per infection cycle) and Omicron spike mutation counts (37 total, 15 in RBD) Proofreading and mutation-rate review.

Recommended additional panels: (1) A diverging effect-size panel for D614G and nsp1 deletions using standardized annotations (direction of effect, assay system, confidence tier), since no common quantitative unit exists across them — do not invent normalized values; (2) a grouped bar chart of Omicron spike mutation counts (total vs RBD) annotated with the ACE2 salt-bridge/hydrogen-bond mechanism Omicron spike mutation counts; (3) optionally a transmissibility comparison (R0: SARS-CoV-2 4.18, Influenza 1.68, Rhinovirus 1.88) contextualized as outcome correlates, not mutation effects per se.

Critical caveats to annotate on every figure: D614G effects come from hamsters, Vero E6, Calu-3, and primary airway tissues with non-randomized animal experiments and no blinding; nsp1 findings use a WA1 backbone that may not generalize to Omicron; the mutation-rate review is a non-systematic student review citing preprints, so rates should be cross-checked before publication use. The Bioinformatics Wizard code below implements this pipeline reproducibly.