HGTstart · interactive results

Zizipju

Candidate evidence, functional annotation and interactive gene trees

Report build: 2026-11-11 12:52 UTC

1 / 1Candidates
1 / 1OGFamily assigned
0 / 1Swiss-Prot mapped
1 / 1GO annotated
1 / 1eggNOG annotated
1 / 1KEGG annotated

These are candidates, not confirmed biological positives. Tree and detail panels are generated only when opened. The table below and every gene detail use the same final annotation table.

Download final tableCandidate summaryFlanking context

1. HGT summary

OGFamily uses the native HOG when available; otherwise it uses a uniquely assigned global EXF. EXF denotes a similarity family, not a proven ortholog group. Family assignment evidence

Scroll horizontally for all columns and vertically for candidates. Click an annotation or Details to inspect its source. Descriptions and KO assignments retain source evidence. Direct gene mappings and Swiss-Prot homology transfers are distinguished in Details; unavailable assignments remain NA.

2. Flanking gene diagram

Hit in a different taxonomic groupHit in the same taxonomic groupScaffold boundaryHGT candidate / shared locusHGT singleton candidateNo classifiable hit evidence
UP1HGTDOWN1XP_015873120.1UP1 | XP_015873130.1 | Hit in the same taxonomic groupHGT | XP_015873120.1 | HGT candidate / shared locusDOWN1 | XP_015873135.1 | Hit in the same taxonomic group
How to read this diagram

Hover over a block for the gene ID, position and classification. Blocks show ordered loci, not physical distances or strand orientation. Yellow in retained earlier results means missing classifiable evidence, not necessarily a completed zero-hit search. New hit-aware filtering skips completed no-hit/unclassifiable coding loci and extends outward; this report does not silently reselect old results.

Download diagram data (TSV)

3. Interactive trees

Tree display and rooting notes

Open a tree from the summary. The initial view uses the saved analysis root, keeps paths to the query and MSMH_OUT reference visible, and collapses other clades of four or more tips. Mixed-taxonomy clades are explicitly labelled. Click internal nodes to expand or collapse; drag to pan and use the wheel to zoom.

Root status: 0 unique MAD roots; 1 ambiguous MAD roots. A displayed root is not proof that its position is uniquely resolved. Alternative-root views and display changes do not change the reported HGT direction, scores or dates.

4. Compare (HGT vs CORE vs MMSH)

HGT vs CORE vs MMSH_OUT homologs

2026-11-11T12:52:35.191256 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. prot_len — Protein length (amino acids). HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. cds_gc — CDS GC content (%). HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. gc_skew — GC skew = (G−C)/(G+C); strand asymmetry / replication-direction signal. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. cpg — CpG dinucleotide frequency — methylation-suppression signal (host-assimilation trace). HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. tpa — TpA dinucleotide frequency — thermostability signal. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. rscu_dist — Relative Synonymous Codon Usage distance to host preference. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. pfam_n — Significant Pfam domain matches (sequence and independent-domain E <= 1e-5, domain GA when available, bias <= score). Overlapping models may count separately. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. pfam_types — Number of distinct Pfam domain types. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. domain_density — Significant Pfam domain matches per residue (pfam_n / prot_len); overlapping models may count separately. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. MMSH_OUT — Outside-homolog representative used for taxonomic association; direction may remain unresolved.; CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference.; HGT — Horizontally transferred gene — the query gene detected as transferred.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
prot_lenHGT1381.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
prot_lenCORE32557.78125506.93034HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
prot_lenMMSH1391.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cds_gcHGT10.46540HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cds_gcCORE320.4436190.020576HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cds_gcMMSH10.57570HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
gc_skewHGT10.08310HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
gc_skewCORE320.1179560.088247HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
gc_skewMMSH10.01330HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cpgHGT10.0170090HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cpgCORE320.0253830.009488HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
cpgMMSH10.0740430HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
tpaHGT10.0434020HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
tpaCORE320.04480.005136HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
tpaMMSH10.0289360HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
rscu_distHGT12.65790HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
rscu_distCORE323.1560661.174393HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
rscu_distMMSH16.81230HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_nHGT11.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_nCORE321.906251.227622HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_nMMSH11.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_typesHGT11.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_typesCORE321.781250.97499HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
pfam_typesMMSH11.00HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
domain_densityHGT10.0026250HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
domain_densityCORE320.0047450.00314HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
domain_densityMMSH10.0025580HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
intron_nHGT12.00HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_nCORE309.73333311.476913HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_nMMSH12.00HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_gcHGT10.31130HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_gcCORE300.3141070.019128HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_gcMMSH10.39660HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_lenHGT1775.50HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_lenCORE30360.134333140.777365HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_lenMMSH11038.00HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_pptHGT10.51670HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_pptCORE300.58420.045913HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_pptMMSH10.53330HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_bpHGT10.00HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_bpCORE300.6247630.255232HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested
intron_bpMMSH10.00HGT/CORE: Mann-Whitney U, n=1/24, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=24/1, Holm p=not tested

Codon usage & composition

2026-11-11T12:52:34.227933 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. cds_gc — CDS GC content (%). eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. gc_skew — GC skew = (G−C)/(G+C); strand asymmetry / replication-direction signal. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. cpg — CpG dinucleotide frequency — methylation-suppression signal (host-assimilation trace). eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. tpa — TpA dinucleotide frequency — thermostability signal. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. rscu_dist — Relative Synonymous Codon Usage distance to host preference.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
cds_gceukhgt10.46540eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
cds_gccore320.4436190.020576eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
gc_skeweukhgt10.08310eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
gc_skewcore320.1179560.088247eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
cpgeukhgt10.0170090eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
cpgcore320.0253830.009488eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
tpaeukhgt10.0434020eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
tpacore320.04480.005136eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
rscu_disteukhgt12.65790eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
rscu_distcore323.1560661.174393eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested

Function motif (Pfam)

2026-11-11T12:52:35.657024 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. pfam_n — Significant Pfam domain matches (sequence and independent-domain E <= 1e-5, domain GA when available, bias <= score). Overlapping models may count separately. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. pfam_types — Number of distinct Pfam domain types. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. domain_density — Significant Pfam domain matches per residue (pfam_n / prot_len); overlapping models may count separately. Pfam — Pfam protein domain database (Pfam-A family).
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
pfam_neukhgt11.00eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
pfam_ncore321.906251.227622eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
pfam_typeseukhgt11.00eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
pfam_typescore321.781250.97499eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
domain_densityeukhgt10.0026250eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
domain_densitycore320.0047450.00314eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested

Gene structure

2026-11-11T12:52:36.750499 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. prot_len — Protein length (amino acids). eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. exon_n — Number of exons. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. ss5_score — 5' splice-site consensus score. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. ss3_score — 3' splice-site consensus score.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
prot_leneukhgt1381.00eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
prot_lencore32557.78125506.93034eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
exon_neukhgt15.00eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
exon_ncore3211.0937511.504163eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
ss5_scoreeukhgt10.16670eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
ss5_scorecore320.3904160.219179eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
ss3_scoreeukhgt10.1250eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
ss3_scorecore320.4004190.282074eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested

Intron features

2026-11-11T12:52:38.193109 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
intron_neukhgt12.00eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_ncore309.73333311.476913eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_gceukhgt10.31130eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_gccore300.3141070.019128eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_leneukhgt1775.50eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_lencore30360.134333140.777365eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_ppteukhgt10.51670eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_pptcore300.58420.045913eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_bpeukhgt10.00eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_bpcore300.6247630.255232eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_relposeukhgt10.55870eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
intron_relposcore300.5253770.098068eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested

Adaptive evolution (dN/dS)

2026-11-11T12:52:39.453440 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ dnds — dN/dS (Ka/Ks) ratio — selection pressure since transfer (<1 purifying, >1 positive). dnds — dN/dS (Ka/Ks) ratio — selection pressure since transfer (<1 purifying, >1 positive). dN/dS — dN/dS (Ka/Ks) ratio — selection pressure since transfer (<1 purifying, >1 positive). dN/dS — dN/dS (Ka/Ks) ratio — selection pressure since transfer (<1 purifying, >1 positive).
Download PDF Download plot data (TSV) Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypevalue
dndsHGT0.0858202

Summary table

featureprohgteukhgtvirhgthgtcore
gc_skewNA0.0831NANA0.118
cds_gcNA0.4654NANA0.4436
cpgNA0.017NANA0.0254
tpaNA0.0434NANA0.0448
prot_lenNA381.0NANA557.7812
rscu_distNA2.6579NANA3.1561
utr5NANANANANA
utr3NANANANANA
exon_nNA5.0NANA11.0938
ss5_scoreNA0.1667NANA0.3904
ss3_scoreNA0.125NANA0.4004
pfam_nNA1.0NANA1.9062
pfam_typesNA1.0NANA1.7812
domain_densityNA0.0026NANA0.0047
dndsNA0.0858NANANA
intron_nNA2.0NANA9.7333
intron_gcNA0.3113NANA0.3141
intron_lenNA775.5NANA360.1343
intron_pptNA0.5167NANA0.5842
intron_bpNA0.0NANA0.6248
intron_p0NA0.5NANA0.648
intron_p1NA0.0NANA0.2263
intron_p2NA0.5NANA0.1257
intron_relposNA0.5587NANA0.5254
intron_gtagNA1.0NANA0.9736
intron_gcagNA0.0NANA0.0088
intron_atacNA0.0NANA0.0067
intron_noncanonNA0.0NANA0.0108

5. Codon usage

Effective number of codons (Nc)

2026-11-11T12:52:33.774935 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. Nc — Effective Number of Codons (20–61) — codon usage bias; lower = stronger bias. Nc — Effective Number of Codons (20–61) — codon usage bias; lower = stronger bias.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
Nceukhgt151.390eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Nccore3253.3268753.69364eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested

Codon usage indices

2026-11-11T12:52:34.817164 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. CAI — Codon Adaptation Index (0–1) — similarity to highly expressed gene codon usage. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. GC3s — GC content at synonymous third-codon positions. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. GC — Overall GC content of the CDS. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. Gravy — Grand Average of Hydropathy — mean hydrophobicity of the protein. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. Aromo — Aromaticity — frequency of aromatic amino acids (Phe+Tyr+Trp). eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. CBI — Codon Bias Index — degree of codon usage bias relative to uniform usage. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. Fop — Frequency of Optimal codons — proportion of optimal codons used. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference.; HGT — Horizontally transferred gene — the query gene detected as transferred.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
CAIeukhgt10.2130eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
CAIcore320.2006250.016951eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
GC3seukhgt10.3610eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
GC3score320.4016250.060679eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
GCeukhgt10.4640eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
GCcore320.4449370.021283eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Gravyeukhgt1-0.1230970eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Gravycore32-0.4669470.445488eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Aromoeukhgt10.083990eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Aromocore320.0803360.025107eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
CBIeukhgt1-0.040eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
CBIcore32-0.0715310.049477eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Fopeukhgt10.3940eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested
Fopcore320.3773750.029369eukhgt/core: Mann-Whitney U, n=1/25, Holm p=not tested

Codon usage: HGT vs CORE vs MMSH_OUT

2026-11-11T12:52:34.653412 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. CAI — Codon Adaptation Index (0–1) — similarity to highly expressed gene codon usage. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. CBI — Codon Bias Index — degree of codon usage bias relative to uniform usage. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. Fop — Frequency of Optimal codons — proportion of optimal codons used. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. Nc — Effective Number of Codons (20–61) — codon usage bias; lower = stronger bias. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. GC3s — GC content at synonymous third-codon positions. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. GC — Overall GC content of the CDS. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. Gravy — Grand Average of Hydropathy — mean hydrophobicity of the protein. HGT — Horizontally transferred gene — the query gene detected as transferred. CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference. MMSH — Outside-homolog representative sequence; association does not establish transfer direction. Aromo — Aromaticity — frequency of aromatic amino acids (Phe+Tyr+Trp). MMSH_OUT — Outside-homolog representative used for taxonomic association; direction may remain unresolved.; CORE — Core gene set (BUSCO single-copy orthologs) — the host-native reference.; HGT — Horizontally transferred gene — the query gene detected as transferred.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
CAIHGT10.2130HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
CAICORE320.2006250.016951HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
CAIMMSH10.2280HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
CBIHGT1-0.040HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
CBICORE32-0.0715310.049477HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
CBIMMSH10.1070HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
FopHGT10.3940HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
FopCORE320.3773750.029369HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
FopMMSH10.480HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
NcHGT151.390HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
NcCORE3253.3268753.69364HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
NcMMSH150.310HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GC3sHGT10.3610HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GC3sCORE320.4016250.060679HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GC3sMMSH10.6530HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GCHGT10.4640HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GCCORE320.4449370.021283HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GCMMSH10.5760HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GravyHGT1-0.1230970HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GravyCORE32-0.4669470.445488HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
GravyMMSH1-0.2409210HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
AromoHGT10.083990HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
AromoCORE320.0803360.025107HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested
AromoMMSH10.0843990HGT/CORE: Mann-Whitney U, n=1/25, Holm p=not tested; HGT/MMSH: Wilcoxon signed-rank, n=1/1, Holm p=not tested; CORE/MMSH: Mann-Whitney U, n=25/1, Holm p=not tested

6. Intron statistics

Intron proportions & scores

2026-11-11T12:52:33.982165 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. gc_content — Intron GC content (%). eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. ppt_score — Polypyrimidine tract score — strength of the intron 3' splice signal. eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. rel_position — Relative position of the intron within the gene.
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
gc_contenteukhgt131.130eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
gc_contentcore3031.2607491.988372eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
ppt_scoreeukhgt10.51650eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
ppt_scorecore300.5822870.047528eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
rel_positioneukhgt10.55870eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
rel_positioncore300.5210580.099779eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested

Intron length

2026-11-11T12:52:34.797266 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ eukhgt — Eukaryote-associated candidate: MSMH_OUT is eukaryotic, irrespective of unresolved direction. length — Intron length (bp). length — Intron length (bp).
Download PDF Download plot data (TSV) Download pairwise tests Download summary statistics
Notes and summary statistics

Points and displayed n count protein IDs (MMSH: unique outside homologs). Where the locus map is present, tests average transcript isoforms per physical locus; loci shared across cohorts are excluded from tests. Two-sided tests, Holm adjustment across all estimable pairs within each feature; alpha=0.05. Different letters indicate a rejected pairwise null; shared letters mean not rejected, not equivalence. n<3: no test. Exploratory comparisons do not correct for phylogenetic dependence. Reused outside homologs are counted once; matched query values are averaged per outside homolog for paired tests.

The plot-data TSV contains one row per displayed point, with its protein/reference ID, group, value and source records. Intron points are means per protein; their constituent intron IDs and values are included. Statistical tests may aggregate points by locus; see the pairwise-test file.

featuretypenmeanstdletterspairwise_tests
lengtheukhgt1775.50eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
lengthcore30366.731112140.114049eukhgt/core: Mann-Whitney U, n=1/24, Holm p=not tested
typetotal_genesgenes_with_intronsintron_gene_ratio_pcttotal_intronsavg_introns_per_geneintrons_with_hitsintrons_with_hits_ratio_pctself_hit_intronsself_hit_ratio_pctavg_gc_contentavg_lengthavg_ppt_scorebranch_point_ratiophase_0_pctphase_1_pctphase_2_pctavg_rel_positionsplice_GT-AGsplice_GC-AGsplice_AT-ACsplice_non-canonicalexon_hitsintergenic_hits
prohgt000.0000.0000.0000.000.000.00.0000.0000.00.00.00.5000000000
eukhgt000.0000.0000.0000.000.000.00.0000.0000.00.00.00.5000000000
hgt11100.0022.0000.002100.0031.13775.50.5170.00050.00.050.00.5587200000
core323093.752879.573612.5414149.1331.04344.10.5950.62465.223.711.10.5050281321036
NA25552555100.00155356.089456.081005664.7330.82417.10.5790.63061.519.119.40.502815003276172392111312

7. Functional enrichment: HGT relative to CORE

AnnotationHGT lociCORE lociTestsFDR < 0.05
GO biological process1/120/25960
GO molecular function1/117/25290
GO cellular component1/120/25430
KEGG pathways0/113/2500
eggNOG functional categories1/119/2560

KEGG pathways: the pathway mapping cache is incomplete. No enrichment P values were computed for this namespace. Public KEGG cross-reference lookups may be retried when the KEGG service is reachable.

GO biological process

2026-11-11T12:52:40.885751 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ 0 20 40 60 80 100 Annotated loci (%) DNA-templated transcription [GO:0006351] regulation of biosynthetic process [GO:0009889] regulation of gene expression [GO:0010468] regulation of macromolecule biosynthetic process [GO:0010556] cellular component organization [GO:0016043] regulation of metabolic process [GO:0019222] regulation of macromolecule metabolic process [GO:0060255] regulation of biological process [GO:0050789] regulation of cellular process [GO:0050794] biological regulation [GO:0065007] cellular component organization or biogenesis [GO:0071840] RNA metabolic process [GO:0016070] a CORE HGT candidates 0.0 0.5 1.0 1.5 -log10(BH-adjusted P) b Filled: FDR < 0.05 Point area: HGT locus count GO biological process | HGT relative to CORE Annotated loci: HGT 1/1; CORE 20/25. 96 terms tested; 0 at FDR < 0.05.
PDF · SVG · Plot data (TSV) · All enrichment tests · Contributing genes
Methods and interpretation

One physical coding locus; annotations unioned across its isoforms; shared HGT/CORE loci excluded. One-sided Fisher exact test (HGT enrichment), BH across all tested terms in each namespace; combined term count >=2 before testing. Loci with usable annotations in each namespace; no-hit, no-term and unresolved mapping excluded. All-locus sensitivity is also reported. is_a and part_of closure; obsolete terms resolve only with one replacement; three roots omitted. Exact Swiss-Prot KEGG gene to organism pathway links; pathways normalized to map IDs. Global maps 01100, 01110 and 01120 omitted. Exact KOG/COG IDs to NCBI functional-category letters; unmapped ENOG identifiers excluded, not guessed. Exploratory comparison with conserved BUSCO-derived CORE, not the whole genome. Homology-transferred annotations, unequal coverage and evolutionary dependence limit causal inference. HGT labels are candidates.

Point coordinates and exact counts are supplied for every displayed term. The contributor file links each term to coding loci and protein identifiers. Unfilled points are not significant; there is no forced enrichment.

GO molecular function

2026-11-11T12:52:41.594370 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ 0 20 40 60 80 100 Annotated loci (%) catalytic activity, acting on a protein [GO:0140096] zinc ion binding [GO:0008270] transition metal ion binding [GO:0046914] cation binding [GO:0043169] metal ion binding [GO:0046872] hydrolase activity [GO:0016787] small molecule binding [GO:0036094] ion binding [GO:0043167] catalytic activity [GO:0003824] binding [GO:0005488] a CORE HGT candidates 0.0 0.5 1.0 1.5 -log10(BH-adjusted P) b Filled: FDR < 0.05 Point area: HGT locus count GO molecular function | HGT relative to CORE Annotated loci: HGT 1/1; CORE 17/25. 29 terms tested; 0 at FDR < 0.05.
PDF · SVG · Plot data (TSV) · All enrichment tests · Contributing genes
Methods and interpretation

One physical coding locus; annotations unioned across its isoforms; shared HGT/CORE loci excluded. One-sided Fisher exact test (HGT enrichment), BH across all tested terms in each namespace; combined term count >=2 before testing. Loci with usable annotations in each namespace; no-hit, no-term and unresolved mapping excluded. All-locus sensitivity is also reported. is_a and part_of closure; obsolete terms resolve only with one replacement; three roots omitted. Exact Swiss-Prot KEGG gene to organism pathway links; pathways normalized to map IDs. Global maps 01100, 01110 and 01120 omitted. Exact KOG/COG IDs to NCBI functional-category letters; unmapped ENOG identifiers excluded, not guessed. Exploratory comparison with conserved BUSCO-derived CORE, not the whole genome. Homology-transferred annotations, unequal coverage and evolutionary dependence limit causal inference. HGT labels are candidates.

Point coordinates and exact counts are supplied for every displayed term. The contributor file links each term to coding loci and protein identifiers. Unfilled points are not significant; there is no forced enrichment.

GO cellular component

2026-11-11T12:52:42.246731 image/svg+xml Matplotlib v3.10.9, https://matplotlib.org/ 0 20 40 60 80 100 Annotated loci (%) nucleus [GO:0005634] cytoplasm [GO:0005737] organelle [GO:0043226] membrane-bounded organelle [GO:0043227] intracellular organelle [GO:0043229] intracellular membrane-bounded organelle [GO:0043231] intracellular anatomical structure [GO:0005622] cellular anatomical structure [GO:0110165] a CORE HGT candidates 0.0 0.5 1.0 1.5 -log10(BH-adjusted P) b Filled: FDR < 0.05 Point area: HGT locus count GO cellular component | HGT relative to CORE Annotated loci: HGT 1/1; CORE 20/25. 43 terms tested; 0 at FDR < 0.05.
PDF · SVG · Plot data (TSV) · All enrichment tests · Contributing genes
Methods and interpretation

One physical coding locus; annotations unioned across its isoforms; shared HGT/CORE loci excluded. One-sided Fisher exact test (HGT enrichment), BH across all tested terms in each namespace; combined term count >=2 before testing. Loci with usable annotations in each namespace; no-hit, no-term and unresolved mapping excluded. All-locus sensitivity is also reported. is_a and part_of closure; obsolete terms resolve only with one replacement; three roots omitted. Exact Swiss-Prot KEGG gene to organism pathway links; pathways normalized to map IDs. Global maps 01100, 01110 and 01120 omitted. Exact KOG/COG IDs to NCBI functional-category letters; unmapped ENOG identifiers excluded, not guessed. Exploratory comparison with conserved BUSCO-derived CORE, not the whole genome. Homology-transferred annotations, unequal coverage and evolutionary dependence limit causal inference. HGT labels are candidates.

Point coordinates and exact counts are supplied for every displayed term. The contributor file links each term to coding loci and protein identifiers. Unfilled points are not significant; there is no forced enrichment.

Annotation coverage and provenance

HGT and CORE proteins were searched together with the same Swiss-Prot index, accession map, DIAMOND and parameters. These enrichment annotations are a separate matched comparison; the main candidate table is unchanged.

Coverage Per-protein evidence Methods, resources and all results
Interpretation notes

INnode and OUTnode label the query side and partner side without assuming transfer direction. DirectionScore describes support across recorded root scenarios, not a posterior probability. Conditional timeHGT values estimate within-recipient gene divergence, not the transfer instant; inspect age-bound sensitivity in Details.

proHGT and eukHGT compare the taxonomy of MSMH_OUT independently of inferred transfer direction; an outside-homolog association is not a confirmed donor. MMSH CDS features require a verified protein/CDS match. Features with unavailable or inconsistent CDS remain missing. Protein length and directly scanned Pfam features can still be compared. CodonW indices use the same reference settings for query and MMSH. Intron comparisons use one mean per gene.

EXF IDs represent global sequence-similarity families, not proven orthogroups or duplication events. Swiss-Prot terms are homology-based transfers. Missing evidence stays NA.