Output Interpretation Guide (HTML, JSON, TSV)

ResistanceProfiler produces one required output and optional structured exports.

Start with the HTML report

Use the HTML report first for interpretation context, then use JSON/TSV for automation and downstream processing.

HTML report (*.report.html)

What to inspect first:

• sample and project identity
• total hits and matched rules
• per-feature mutation details and consequences
• phenotype and clinical phenotype context
• optional manual classifications

Best use:

• review by analysts and clinicians
• sharing a portable report artifact

Detailed examples of important report tabs

Primary summary that condenses findings.

Detailed overview over all mutations that have rule hits in the selected database.

Detailed overview over all mutations independent on whether they have database hits.

JSON export (*.results.json)

Structured machine-readable export for automation and reproducibility.

Top-level sections include:

• run
• variant_result
• coverage_gap
• formula_rule_hit
• sample_classification

Best use:

• downstream pipelines
• archival and deterministic regeneration
• data integration with external systems

Reproducible artifacts

JSON exports are intended as reproducible artifacts and can be used directly with respro regenerate --json.

Regenerate a report from JSON:

respro regenerate \
  --project myrespro.db \
  --json my_output/sample_variants.results.json \
  --output my_output

See CLI Reference for all regeneration options.

TSV export (*.results.tsv)

A denormalized, tab-separated table of every annotated variant and its matched resistance rules. One row is emitted per (annotated variant × matched rule); variants with no matching rule still appear with empty rule columns. This mirrors the HTML Database Hits table but is flat and machine-readable.

Enable it with --export tsv (repeatable, combinable with json/pdf):

respro vcf \
  --project myrespro.db \
  --vcf sample.vcf \
  --ref-fasta reference.fa \
  --output my_output \
  --export tsv

Columns

Column	Description
reference	Matched internal reference name (VCF mode only; omitted in FASTA mode). Populated for multi-species VCF runs; empty for single-reference runs where the chrom is not the reference accession.
gene	Feature / gene name (display name applied when configured).
nt_mut	Nucleotide change on the internal reference, ref{pos}alt (1-based). Combined codon events use ref_codon{codon_pos}alt_codon.
nt_mut_user	Nucleotide change on the user-supplied reference (VCF coords before remap). VCF mode only; omitted in FASTA mode.
aa_effect	Amino-acid change ref_aa{codon_pos}alt_aa (1-based). INS_any (...) prefix for wildcard insertion rules.
strand	Coding strand of the feature (+/-), sourced from the feature record.
af	Allele frequency (raw float).
af_bin	AF bin label (e.g. low/moderate/high).
depth	Read depth at the variant (VCF mode only; omitted in FASTA mode). Empty for combined formula rows.
consequence	Consequence label (missense, frameshift, …).
in_database	yes when at least one rule matched (single or formula member); otherwise no.
rule_type	single, formula, formula-member, or n/a for non-hits.
drug	Drug name for the matched rule. n/a for non-hits.
phenotype	Rule phenotype (resistant/intermediate/sensitive/…). n/a for non-hits.
clinical_phenotype	Clinical phenotype. n/a for non-hits.
ic50	Rule IC50 value (string, may carry qualifiers). Empty for non-hits.
fold_ic50	Rule fold-IC50 value. Empty for non-hits.
score	Rule score. Empty for non-hits.
source	Rule source. n/a for non-hits.
publications	|-joined publication identifiers (DOI, or PubMed ID as fallback). Empty for non-hits.

Row semantics

• Single rules: one row per matching rule. A variant conferring resistance to two drugs produces two rows, each carrying that rule's own phenotype/IC50/fold-IC50/score.
• Formula (combinatorial) rules: one combined row per fired formula rule. Member mutations are joined with ; in gene, nt_mut, nt_mut_user, aa_effect, af, af_bin, and strand. The phenotype/IC50/fold-IC50/score come from the formula rule set (the combined call), not the individual members.
• Formula-member-only variants: a variant that is only a formula member (no single rule of its own) gets a rule_type=formula-member row with in_database=yes and empty rule metric columns.
• Effect-as-resistant: metadata-only synthetic hits (e.g. frameshifts classified as resistant by algorithm config) appear as rule_type=single rows with source=Metadata algorithm.

Web download

In the webapp, the TSV is produced for every profile/regenerate run alongside the HTML, PDF, and JSON artifacts. Download it from the Analyze tab (single-report action bar), the Reports tab (per-row TSV link), or the batch/session "Download all" zip bundles. Run the CLI with --export tsv for command-line use.