AMAP: Assisted Microbial Annotation Pipeline Report
AMAP v1.0.1
18/10/2026
Overview
Dataset Composition
This section provides a general overview of the dataset, showing the distribution of sequences across lineages/groups.
Sample Quality Overview
Per-sample summary of total CDS, correction rates, and missing reference genes.
Annotation Quality Metrics
Per-sample assembly and annotation quality: genome size, GC%, coding density, hypothetical %, and functional annotation rate.
Overview Table
Coding Density
Hypothetical %
Genome Size Distribution
AMAP Annotation Results
CDS Distribution per Lineage
CDS not in Reference
CDS Correction Summary
Missing Reference Genes (Rv)
Reference genes absent from the Bakta annotation and recovered by AMAP.
Heatmap
Which Rv genes are missing in which lineages? Darker = missing in more genomes of that lineage.
Full Table
Functional Annotation
COG Categories (EggNOG)
Overview
Statistics
Per COG (% Percentage)
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
NA
Per COG (Nº CDS)
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
NA
Mycobrowser Categories
Mycobrowser functional categories are specific to the M. tuberculosis complex. This section is only shown when Mycobrowser data is available.
Overview
Per Category (%)
intermediary metabolism and respiration
conserved hypotheticals
cell wall and cell processes
lipid metabolism
information pathways
regulatory proteins
PE/PPE
virulence, detoxification, adaptation
insertion seqs and phages
Per Category (Nº CDS)
intermediary metabolism and respiration
conserved hypotheticals
cell wall and cell processes
lipid metabolism
information pathways
regulatory proteins
PE/PPE
virulence, detoxification, adaptation
insertion seqs and phages
Statistics
Compared to Reference
This section compares query genomes against the median distribution across all samples. Deviations indicate genome-specific gains or losses in functional categories.
Overview
Per Category
cell wall and cell processes
conserved hypotheticals
information pathways
insertion seqs and phages
intermediary metabolism and respiration
lipid metabolism
PE/PPE
regulatory proteins
virulence, detoxification, adaptation
Statistics
PE/PPE Gene Families
PE/PPE genes are characteristic of Mycobacteria. This section is only shown when Mycobrowser functional categories are available.
Distribution per Lineage
Statistics
KEGG Pathway Analysis
Distribution of KEGG pathway annotations across lineages.
Top Pathways
Full Table
Pseudogene Detection
Genes without a stop codon in their annotated coordinates — potential pseudogenes.
Per Lineage
Gene Duplications
Gene duplications detected by all-vs-all Diamond BLASTp within and across genomes.
Duplication Summary
48 homologous community pairs detected across all genomes.
Cross-genome Communities
Network Metrics
Pangenome Analysis
Gene presence/absence across samples based on pangene analysis.
Core vs Accessory Genes
Gene Frequency Spectrum
Presence/Absence Heatmap
AMAP CDS Stats
Detailed breakdown of the CDS-correction cases identified by AMAP.
Classification:
- Case 1 keep: CDS missing from the reference — potentially real novel genes
- Case 1 remove: CDS falsely introduced by Bakta, absent from reference
- Case 2: Perfect coordinate match with reference
- Case 3: Same start/end but containing mismatches
- Case 4: Coordinates corrected by AMAP
- Missing Genes: Reference genes recovered by AMAP (not annotated by Bakta)
Boxplot
Violinplot
Histogram Cases
Heatmap
Per-case Statistics
Case 1
Case 1 Keep
Case 1 Remove
Case 2
Case 3
Case 4
Total CDS
Missing Rvs
Master Table Explorer
Interactive explorer for the full annotation master table with all functional annotations.
Report generated by AMAP v1.0.1 on 2026-10-18 15:43.