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
- QC Report 1 — SRR33827285
- QC Report 2 — SRR34028974
- QC Report 3 — SRR34028974
- QC Report 4 — SRR34974705
- QC Report 5 — SRR34974705
- QC Report 6 — ERR311523
- QC Report 7 — ERR311523
- QC Report 8 — ERR311526
- QC Report 9 — ERR311526
- QC Report 10 — SRR33365784
- QC Report 11 — SRR33365784
- QC Report 12 — SRR33624157
- QC Report 13 — SRR33624157
- QC Report 14 — SRR33827285
Read trimming
| Sample | Input Pairs | Both Surviving | Forward Only | Reverse Only | Dropped (%) | Survival Rate (%) |
|---|---|---|---|---|---|---|
| ERR311523 | 2301169 | 2076890 | 160411 | 28474 | 1.54% | 98.46% |
| SRR33827285 | 903731 | 840802 | 24915 | 17501 | 2.27% | 97.73% |
| ERR311526 | 2373456 | 2064005 | 215277 | 45179 | 2.06% | 97.94% |
| SRR33365784 | 1570384 | 1440596 | 66275 | 18811 | 2.85% | 97.15% |
| SRR33624157 | 470738 | 413697 | 39324 | 5409 | 2.61% | 97.39% |
| SRR34974705 | 759101 | 695060 | 44243 | 7637 | 1.60% | 98.40% |
| SRR34028974 | 1515904 | 1352221 | 104026 | 22147 | 2.47% | 97.53% |
Assembly
Assembly statistics
| Sample | Contigs | Total Length | Min Length | Max Length | Avg Length | N50 |
|---|---|---|---|---|---|---|
| ERR311523 | 1400 | 4972438 | 78 | 401701 | 3551 | 120812 |
| ERR311526 | 2602 | 6696807 | 78 | 480095 | 2573 | 130909 |
| SRR33365784 | 716 | 4843593 | 78 | 305284 | 6764 | 153715 |
| SRR33624157 | 394 | 5139664 | 78 | 263082 | 13044 | 109485 |
| SRR33827285 | 329 | 5028038 | 78 | 388708 | 15282 | 111853 |
| SRR34028974 | 771 | 5274637 | 78 | 257080 | 6841 | 109280 |
| SRR34974705 | 243 | 4808709 | 78 | 315052 | 19788 | 137163 |
Annotation
Annotation summary
| Sample ID | Gene Count |
|---|---|
| ERR311523 | 4463 |
| ERR311526 | 5884 |
| SRR33365784 | 4409 |
| SRR33624157 | 4841 |
| SRR33827285 | 4712 |
| SRR34028974 | 5038 |
| SRR34974705 | 4506 |
Pangenome
Pangenome report
Pangenome Analysis
Roary completed successfully. (This page will show Roary results if available.)
Gene Presence/Absence Heatmap
MLST
Combined MLST
| Sample ID | Species | ST | gapA | infB | mdh | pgi | phoE | rpoB | tonB |
|---|---|---|---|---|---|---|---|---|---|
| ERR311523 | ecloacae | 757 | 188 | 107 | 177 | 214 | 153 | 36 | 1 |
| ERR311526 | paeruginosa | 274 | 23 | 5 | 11 | 7 | 1 | 12 | 7 |
| SRR33365784 | ecloacae | 116 | 9 | 4 | 14 | 6 | 11 | 4 | 6 |
| SRR33624157 | ecloacae | 461 | 9 | 4 | 14 | 6 | 37 | 4 | 9 |
| SRR33827285 | ecloacae | - | 192 | 44 | 61 | 1 | 1 | 22 | 1 |
| SRR34028974 | ecloacae | 719 | 234 | 149 | 250 | 278 | 232 | 96 | 156 |
| SRR34974705 | ecloacae | 51 | 4 | 4 | 4 | 6 | 37 | 4 | 6 |
Variants
Variant summary
| Sample | Status | SNPs | INDELs | Total Variants | Attempts |
|---|---|---|---|---|---|
| ERR311523 | Success | 33410 | 0 | 33410 | 1 |
| ERR311526 | Success | 226 | 0 | 226 | 1 |
| SRR33365784 | Success | 116016 | 0 | 116016 | 1 |
| SRR33624157 | Success | 89761 | 0 | 89761 | 1 |
| SRR33827285 | Success | 33729 | 0 | 33729 | 1 |
| SRR34028974 | Success | 106047 | 0 | 106047 | 1 |
| SRR34974705 | Success | 92995 | 0 | 92995 | 1 |
Antimicrobial Resistance
Mobile Genetic Elements
Virulence
BLAST
Phylogeny
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