Recore run report

Phylogeny

Corrected matrixinputcorrectedabsent

Unique synteniesScale

Run details

Summary

8 binary matrix cells were corrected under the Balanced policy from 39 searchable gaps. Recore found the gene in 3 more cells that it kept out of the matrix, 3 by the Balanced policy and 0 by the quality floors, and its synteny and paralog guards rejected 0 candidates. All 11 accepted evidence rows are in orthology_evidence.tsv. Core changed from 14 to 17 clusters (+3); soft-core changed from 14 to 17 (+3).

Output directory: tutorial_out

Using these results

False gene absences in the gene presence/absence matrix (24 clusters, 12 genomes) were corrected with Recore v1.0.0. Each absent cell of a cluster present in at least 10% of genomes was searched by aligning the cluster's representative sequence and every allele to that genome's assembly with minimap2 (preset asm5); a hit counted when it reached at least 90% identity over at least 80% of the query. Hits were classified against the genome annotation as missing annotations, split or fragmented genes, start variants or pseudogenes, and kept only when the flanking gene context (synteny) agreed with the cluster's. Under the balanced matrix policy, 8 cells were set to present; 3 further cells with sequence evidence were kept out of the binary matrix, and the synteny and paralog guards rejected 0 candidates. The evidence behind every corrected and kept-out cell is listed in orthology_evidence.tsv.

3 cells have sequence evidence but are not in the corrected matrix (3 by the Balanced policy, 0 by the quality floors). They are drawn as kept out and carry publication_status held_out_policy or held_out_quality.
11 gaps were never searched (11 in clusters below the 10% prevalence floor). They are absent because the input matrix says so, not because Recore looked: the states file writes them as NOT_SEARCHED and the matrix draws them hatched.

Changed cells

The list of changed cells needs the interactive workspace; orthology_evidence.tsv has every row.

Parameters and command line

Recore: v1.0.0 (recore.outputs.v7)
Report written: 2026-10-18T07:36:56Z
Command line: recore -p tutorial_data/gene_presence_absence.csv -r tutorial_data/pan_genome_reference.fa -g tutorial_data/genomes -a tutorial_data/annotations --synteny --multi-allele --matrix-policy balanced --reference-genome L4_AS00401 --tree tutorial_data/species.tree --write-html-report -o tutorial_out/
Minimum identity: 90%
Minimum query coverage: 80%
Minimum prevalence: 10% of genomes
minimap2 preset: asm5
Matrix policy: Balanced
All alleles as queries: yes
Annotations: supplied
Synteny: on
NSC: off
Reference genome: L4_AS00401
Tree: supplied

Run statistics

Searchable gaps

after filters and FASTA matching

Matrix corrected

rescues + NSC merged cells

Accepted rescues

all accepted evidence rows

Rejected evidence

synteny/paralog guardrails

Core genome

14 → 17

strict core clusters

Soft-core

14 → 17

≥95% prevalence

Orthology actions

corrected8 72.7%

kept out by the matrix policy3 27.3%

Confidence tiers

high8 72.7%

moderate3 27.3%

Evolutionary priorities

highlight23 95.8%

filter or review (unstable)1 4.2%

Genome QC

pass12 100.0%

Dominant mechanisms

ancestral retained no disruption

17 70.8%

clean insertion or acquisition candidate

2 8.3%

deletion loss candidate

2 8.3%

unresolved accessory variation

2 8.3%

pseudogenization

1 4.2%

Top candidate clusters

Cluster	Priority	Score	Mechanism and wording
Rv0001	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0002	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0003	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0004	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0005	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0006	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0007	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0010c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0011c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0012	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0013	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0014c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0015c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0016c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0017c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0019c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0020c	highlight	1.000	ancestral retained no disruptionConsistent with conserved ancestral presence in the analysed tree.
Rv0009	highlight	0.952	pseudogenizationDescribe as disrupted homologous sequence, not as intact gene presence.
Rv1180	highlight	0.940	clean insertion or acquisition candidateCandidate accessory acquisition/insertion relative to the audited reference; validate flanking sequence before claiming a novel locus.
Rv1181	highlight	0.940	clean insertion or acquisition candidateCandidate accessory acquisition/insertion relative to the audited reference; validate flanking sequence before claiming a novel locus.
Rv0018c	highlight	0.924	deletion loss candidatePresence is inferred ancestral with one or more losses; inspect flanks for deletion scars or mobile-element mediation.
Rv0008c	highlight	0.884	deletion loss candidatePresence is inferred ancestral with one or more losses; inspect flanks for deletion scars or mobile-element mediation.
Rv2930	highlight	0.770	unresolved accessory variationEvolutionary process is not resolved from matrix, synteny, reference-event, and optional tree evidence alone.
Rv3810	filter or review (unstable)	0.000	unresolved accessory variationEvolutionary process is not resolved from matrix, synteny, reference-event, and optional tree evidence alone. None of the 11 absences behind this call were searched (the cluster is below --min-prevalence); they are the input matrix's calls, not Recore's.

Click a row, or Tab to it and press Enter, to open that cluster in the matrix.

Files in the output directory

The links open the files beside this report, so they work while the report sits in its output directory.

gene_presence_absence_recore.csvCorrected binary matrix · 24 rows gene_presence_absence_recore.RtabCorrected binary matrix as 1/0, for Rtab readers · 891 B orthology_evidence.tsvEvery rescue and rejected candidate, with its decision and why · 11 rows gene_presence_absence_recore_states.csvMultistate matrix: input, corrected, NSC, kept-out and not-searched codes · 24 rows rescue_report.tsvOne row per rescue: type, identity, coverage and locus · 11 rows genome_qc.tsvPer-genome inputs, correction burden and QC status · 12 rows evolutionary_events.tsvCluster mechanisms, priorities and phylogenetic patterns · 24 rows summary.txtPlain-text run summary · 648 B run_manifest.jsonInputs, parameters, counts and the command line · 1.9 KB cluster_component_members.tsvMembers of each cluster component · 0 rows cluster_components.tsvComponents of related clusters · 0 rows cluster_locus_context.tsvLocus context per cluster and genome · 46 rows cluster_locus_summary.tsvLocus context summary per cluster · 24 rows cluster_relationships.tsvSplit, alias, paralog and NSC links between clusters · 0 rows cluster_synteny_blocks.tsvUnique flanking-gene blocks per cluster · 59 rows reference_genome_audit.tsvReference-absence audit (--reference-genome) · 24 rows