Analysis Summary
This report aggregates results from rMAP modules (QC, assembly/annotation, pangenome/phylogeny, AMR/MGE/virulence/BLAST, and phylogeny).
Quality Control
Per-sample QC reports
Read trimming
| Sample | Input Pairs | Both Surviving | Forward Only | Reverse Only | Dropped (%) | Survival Rate (%) |
|---|---|---|---|---|---|---|
| SRR14477337 | 1082495 | 854314 | 122029 | 31990 | 6.85% | 93.15% |
| SRR14477335 | 1076144 | 845022 | 124532 | 31223 | 7.00% | 93.00% |
| SRR14477334 | 1053572 | 824722 | 123947 | 30677 | 7.05% | 92.95% |
| SRR14477341 | 986915 | 751585 | 133817 | 28137 | 7.43% | 92.57% |
| SRR14477336 | 987113 | 781411 | 109141 | 28653 | 6.88% | 93.12% |
Assembly
Assembly statistics
| Sample | Contigs | Total Length | Min Length | Max Length | Avg Length | N50 |
|---|---|---|---|---|---|---|
| SRR14477334 | 733 | 4928869 | 78 | 329134 | 6724 | 130724 |
| SRR14477335 | 685 | 4926179 | 78 | 329134 | 7191 | 109101 |
| SRR14477336 | 722 | 4927975 | 78 | 329134 | 6825 | 109079 |
| SRR14477337 | 675 | 4960630 | 78 | 270166 | 7349 | 103671 |
| SRR14477341 | 901 | 4945903 | 78 | 329134 | 5489 | 116558 |
Annotation
Annotation summary
| Sample ID | Gene Count |
|---|---|
| SRR14477334 | 4500 |
| SRR14477335 | 4511 |
| SRR14477336 | 4504 |
| SRR14477337 | 4564 |
| SRR14477341 | 4502 |
Pangenome
Pangenome report
Roary completed successfully. If a standalone Roary HTML summary exists, link it here: Open Roary report (hide/remove this link if you don’t generate it).
Gene Presence/Absence Heatmap
MLST
Combined MLST
| Sample ID | Species | ST | gapA | infB | mdh | pgi | phoE | rpoB | tonB |
|---|---|---|---|---|---|---|---|---|---|
| SRR14477334 | ecoli | 58 | 6 | 4 | 4 | 16 | 24 | 8 | 14 |
| SRR14477335 | ecoli | 58 | 6 | 4 | 4 | 16 | 24 | 8 | 14 |
| SRR14477336 | ecoli | 58 | 6 | 4 | 4 | 16 | 24 | 8 | 14 |
| SRR14477337 | ecoli | 58 | 6 | 4 | 4 | 16 | 24 | 8 | 14 |
| SRR14477341 | ecoli | 58 | 6 | 4 | 4 | 16 | 24 | 8 | 14 |
Variants
Variant summary
| Sample | Status | SNPs | INDELs | Total Variants | Attempts |
|---|---|---|---|---|---|
| SRR14477334 | Success | 36884 | 0 | 36884 | 1 |
| SRR14477335 | Success | 36933 | 0 | 36933 | 1 |
| SRR14477336 | Success | 36875 | 0 | 36875 | 1 |
| SRR14477337 | Success | 36951 | 0 | 36951 | 1 |
| SRR14477341 | Success | 36853 | 0 | 36853 | 1 |
Note: The red highlight is just styling (as in the original). Adjust if you only want errors highlighted.
Antimicrobial Resistance
Mobile Genetic Elements
Virulence
BLAST
Phylogeny
Core gene phylogeny
Accessory gene phylogeny
