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 — ERR3569448
- QC Report 2 — ERR3569451
- QC Report 3 — ERR3569451
- QC Report 4 — SRR3666962
- QC Report 5 — SRR3666962
- QC Report 6 — SRR5739056
- QC Report 7 — SRR5739056
- QC Report 8 — SRR6037664
- QC Report 9 — SRR6037664
- QC Report 10 — SRR8289559
- QC Report 11 — ERR1989084
- QC Report 12 — SRR8289559
- QC Report 13 — ERR1989084
- QC Report 14 — ERR1989100
- QC Report 15 — ERR1989100
- QC Report 16 — ERR1989115
- QC Report 17 — ERR1989115
- QC Report 18 — ERR3197698
- QC Report 19 — ERR3197698
- QC Report 20 — ERR3569448
Read trimming
| Sample | Input Pairs | Both Surviving | Forward Only | Reverse Only | Dropped (%) | Survival Rate (%) |
|---|---|---|---|---|---|---|
| ERR1989100 | 2298763 | 1600109 | 75796 | 499018 | 5.39% | 94.61% |
| ERR3569448 | 460892 | 421206 | 26043 | 4605 | 1.96% | 98.04% |
| ERR1989084 | 975120 | 741122 | 30505 | 145673 | 5.93% | 94.07% |
| SRR8289559 | 2966009 | 2727196 | 118451 | 47340 | 2.46% | 97.54% |
| SRR6037664 | 1535181 | 1426617 | 72986 | 16306 | 1.26% | 98.74% |
| ERR1989115 | 2409162 | 2021653 | 84776 | 158282 | 6.00% | 94.00% |
| SRR3666962 | 4199835 | 3740255 | 275813 | 54804 | 3.07% | 96.93% |
| ERR3569451 | 782780 | 737248 | 15669 | 15818 | 1.79% | 98.21% |
| ERR3197698 | 2200212 | 1891256 | 232034 | 18270 | 2.67% | 97.33% |
| SRR5739056 | 629911 | 541262 | 68353 | 6498 | 2.19% | 97.81% |
Assembly
Assembly statistics
| Sample | Contigs | Total Length | Min Length | Max Length | Avg Length | N50 |
|---|---|---|---|---|---|---|
| ERR1989084 | 496 | 4064200 | 78 | 291997 | 8193 | 62937 |
| ERR1989100 | 1452 | 4123115 | 78 | 158287 | 2839 | 50404 |
| ERR1989115 | 664 | 4151841 | 78 | 280824 | 6252 | 75850 |
| ERR3197698 | 814 | 4125945 | 78 | 213627 | 5068 | 40029 |
| ERR3569448 | 430 | 4076798 | 78 | 292457 | 9480 | 66110 |
| ERR3569451 | 437 | 4107193 | 78 | 292646 | 9398 | 66110 |
| SRR3666962 | 15000 | 6820763 | 78 | 247897 | 454 | 15812 |
| SRR5739056 | 398 | 4013282 | 78 | 308553 | 10083 | 75212 |
| SRR6037664 | 928 | 3956862 | 78 | 243391 | 4263 | 57273 |
| SRR8289559 | 534 | 3994036 | 78 | 166464 | 7479 | 61165 |
Annotation
Annotation summary
| Sample ID | Gene Count |
|---|---|
| ERR1989084 | 3783 |
| ERR1989100 | 3792 |
| ERR1989115 | 3881 |
| ERR3197698 | 3824 |
| ERR3569448 | 3817 |
| ERR3569451 | 3854 |
| SRR3666962 | 4452 |
| SRR5739056 | 3719 |
| SRR6037664 | 3599 |
| SRR8289559 | 3692 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ERR1989084 | abaumannii_2 | 1 | 1 | 1 | 1 | 1 | 5 | 1 | 1 |
| ERR1989100 | abaumannii_2 | 71 | 20 | 26 | 26 | 14 | 26 | 16 | 25 |
| ERR1989115 | abaumannii_2 | 1 | 1 | 1 | 1 | 1 | 5 | 1 | 1 |
| ERR3197698 | abaumannii_2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| ERR3569448 | abaumannii_2 | 1 | 1 | 1 | 1 | 1 | 5 | 1 | 1 |
| ERR3569451 | abaumannii_2 | 1 | 1 | 1 | 1 | 1 | 5 | 1 | 1 |
| SRR3666962 | abaumannii_2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| SRR5739056 | abaumannii_2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| SRR6037664 | abaumannii_2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| SRR8289559 | abaumannii_2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
Variants
Variant summary
| Sample | Status | SNPs | INDELs | Total Variants | Attempts |
|---|---|---|---|---|---|
| ERR1989084 | Success | 37374 | 0 | 37374 | 1 |
| ERR1989100 | Success | 90033 | 0 | 90033 | 1 |
| ERR1989115 | Success | 38391 | 0 | 38391 | 1 |
| ERR3197698 | Success | 37047 | 0 | 37047 | 1 |
| ERR3569448 | Success | 36785 | 0 | 36785 | 1 |
| ERR3569451 | Success | 37260 | 0 | 37260 | 1 |
| SRR3666962 | Success | 36030 | 0 | 36030 | 1 |
| SRR5739056 | Success | 37802 | 0 | 37802 | 1 |
| SRR6037664 | Success | 36589 | 0 | 36589 | 1 |
| SRR8289559 | Success | 37164 | 0 | 37164 | 1 |
Antimicrobial Resistance
Mobile Genetic Elements
Virulence
Per-sample Virulence reports
- Virulence Report 1 — SRR8289559
- Virulence Report 2 — ERR1989084
- Virulence Report 3 — ERR1989100
- Virulence Report 4 — ERR1989115
- Virulence Report 5 — ERR3197698
- Virulence Report 6 — ERR3569448
- Virulence Report 7 — ERR3569451
- Virulence Report 8 — SRR3666962
- Virulence Report 9 — SRR5739056
- Virulence Report 10 — SRR6037664
BLAST
Per-sample BLAST reports
Phylogeny
core_core_genes.png
accessory_accessory_genes.png
