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 — SRR24750751
- QC Report 2 — SRR33800821
- QC Report 3 — SRR33800821
- QC Report 4 — SRR33800825
- QC Report 5 — SRR33800825
- QC Report 6 — SRR35035823
- QC Report 7 — SRR35035823
- QC Report 8 — ERR10879137
- QC Report 9 — ERR10879137
- QC Report 10 — ERR10879161
- QC Report 11 — ERR10879161
- QC Report 12 — ERR10879176
- QC Report 13 — ERR10879176
- QC Report 14 — SRR13086356
- QC Report 15 — SRR13086356
- QC Report 16 — SRR24750751
Read trimming
| Sample | Input Pairs | Both Surviving | Forward Only | Reverse Only | Dropped (%) | Survival Rate (%) |
|---|---|---|---|---|---|---|
| SRR24750751 | 871112 | 787733 | 51514 | 13505 | 2.11% | 97.89% |
| ERR10879176 | 2569983 | 2330540 | 113335 | 63565 | 2.43% | 97.57% |
| SRR33800825 | 2905992 | 2706272 | 167569 | 9781 | 0.77% | 99.23% |
| ERR10879137 | 2797304 | 2540603 | 130882 | 61356 | 2.30% | 97.70% |
| SRR13086356 | 732455 | 659691 | 54966 | 6009 | 1.61% | 98.39% |
| SRR35035823 | 1505767 | 1474488 | 9378 | 2915 | 1.26% | 98.74% |
| ERR10879161 | 3089210 | 2777702 | 166347 | 66023 | 2.56% | 97.44% |
| SRR33800821 | 3937151 | 3584551 | 308695 | 12334 | 0.80% | 99.20% |
Assembly
Assembly statistics
| Sample | Contigs | Total Length | Min Length | Max Length | Avg Length | N50 |
|---|---|---|---|---|---|---|
| ERR10879137 | 1149 | 5293130 | 78 | 277360 | 4606 | 60107 |
| ERR10879161 | 1239 | 5223128 | 78 | 378297 | 4215 | 60707 |
| ERR10879176 | 1197 | 5383130 | 78 | 295834 | 4497 | 68263 |
| SRR13086356 | 530 | 4612919 | 78 | 269806 | 8703 | 67377 |
| SRR24750751 | 14258 | 15783011 | 78 | 201661 | 1106 | 5731 |
| SRR33800821 | 2135 | 5582326 | 78 | 413334 | 2614 | 55262 |
| SRR33800825 | 1182 | 5602655 | 78 | 223126 | 4739 | 80314 |
| SRR35035823 | 2585 | 5780534 | 78 | 172513 | 2236 | 58714 |
Annotation
Annotation summary
| Sample ID | Gene Count |
|---|---|
| ERR10879137 | 4924 |
| ERR10879161 | 4824 |
| ERR10879176 | 4974 |
| SRR13086356 | 4234 |
| SRR24750751 | 13851 |
| SRR33800821 | 4994 |
| SRR33800825 | 5118 |
| SRR35035823 | 5283 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ERR10879137 | ecoli | 10 | 10 | 11 | 4 | 8 | 8 | 8 | 2 |
| ERR10879161 | ecoli | 10 | 10 | 11 | 4 | 8 | 8 | 8 | 2 |
| ERR10879176 | ecoli | 2223 | 6 | 11 | 5 | 8 | 7 | 8 | 2 |
| SRR13086356 | ecoli | 10 | 10 | 11 | 4 | 8 | 8 | 8 | 2 |
| SRR24750751 | ecoli | 2541 | 148 | 29 | 33 | 16 | 11 | 8 | 41 |
| SRR33800821 | ecoli | 1011 | 6 | 4 | 159 | 44 | 112 | 1 | 17 |
| SRR33800825 | ecoli | 69 | 21 | 35 | 27 | 6 | 5 | 5 | 4 |
| SRR35035823 | ecoli | 21 | 16 | 4 | 12 | 16 | 9 | 7 | 7 |
Variants
Variant summary
| Sample | Status | SNPs | INDELs | Total Variants | Attempts |
|---|---|---|---|---|---|
| ERR10879137 | Success | 3895 | 0 | 3895 | 1 |
| ERR10879161 | Success | 6972 | 0 | 6972 | 1 |
| ERR10879176 | Success | 24720 | 0 | 24720 | 1 |
| SRR13086356 | Success | 127 | 0 | 127 | 1 |
| SRR24750751 | Success | 25057 | 0 | 25057 | 1 |
| SRR33800821 | Success | 44520 | 0 | 44520 | 1 |
| SRR33800825 | Success | 59551 | 0 | 59551 | 1 |
| SRR35035823 | Success | 37423 | 0 | 37423 | 1 |
Antimicrobial Resistance
Mobile Genetic Elements
Virulence
BLAST
Phylogeny
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