Plasmid Virus Metrics

Plasmid_Fraction

Fraction of total contigs with plasmid_score >= 0.75. Uses Binette contig_count as denominator, not plasmid_summary.tsv row count.

Plasmid_Length_Weighted_Score

Length-weighted mean of plasmid_score across contigs: sum(score_i * length_i) / sum(length_i). Falls back to simple mean if lengths unavailable. In plasmid TSV output, column is renamed to Length_Weighted_Score.

Plasmid_Signal_Uniformity

Measures how uniformly the plasmid signal is distributed across contigs. Uses the same scoring as PlasMAAG (Lindez et al. 2026):

Level	Length-Weighted Score	Minimum Score
High	>= 0.9	>= 0.8
Medium	>= 0.7	>= 0.5
Low	below Medium thresholds

High uniformity suggests all contigs carry a strong plasmid signal, consistent with a single replicon without chromosomal contamination.

Virus_Length_Weighted_Score

Length-weighted mean of virus_score across contigs. In virus TSV output, renamed to Length_Weighted_Score.

Virus_Signal_Uniformity

Analogous to plasmid uniformity, but proviruses reduce confidence. An integrated prophage within a chromosomal bin produces a less informative viral signal (Camargo et al. 2024).

Level	Length-Weighted Score	Minimum Score	Proviruses
High	>= 0.9	>= 0.8	None
Medium	High scores with proviruses present, OR moderate signal (>= 0.7 / >= 0.5)		Any
Low	below Medium thresholds		Any

Provirus Handling

Column	Description
Provirus_Count	Contigs with topology == Provirus; potentially integrated into the bin
Provirus_Fraction	provirus_count / virus_count

Proviruses are common in bacterial chromosomes and do not trigger Virus_MAG classification when completeness >= 50%.

Mobility_Potential

Pipe-separated evidence summary. Components appended only if present; none if no MGE evidence:

plasmid:High|virus:Low|proviruses:2|mob:Relaxed,Mobilized

The mob types come from geNomad plasmid_summary.tsv.