Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate | Predicted Mutations | Mean Coverage | Total Reads | Percent Mapped | Mapped Reads | Average Read Length |
|---|---|---|---|---|---|---|
| A13 F1 I1 R1 | 778 | 68.7 | 3228504 | 93.4% | 3015422 | 109.7 |
Breseq alignment
| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 2,995,314 | C→T | pseudogene (447/447 nt) | ygeN ← | pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,995,314 | 0 | C | T | 100.0% | 119.9 / NA | 38 | pseudogene (447/447 nt) | ygeN | pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/18); total (20/18) | |||||||||||
TGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGG > NC_000913/2995183‑2995432 | tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAg > 1:528436/1‑139 (MQ=255) acaGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAc > 1:51711/1‑139 (MQ=255) aaaaaTCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTGAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa < 1:1075678/139‑1 (MQ=255) atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCa < 2:845918/123‑1 (MQ=255) atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCa > 1:845918/1‑123 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa > 2:634969/1‑69 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa < 1:634969/69‑1 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCa < 1:1414148/113‑1 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCa > 2:1414148/1‑113 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCa > 1:1464105/1‑139 (MQ=255) ttAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc < 1:1080397/59‑1 (MQ=255) ttAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc > 2:1080397/1‑59 (MQ=255) ttAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGAttt > 1:1165849/1‑139 (MQ=255) aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg > 2:339145/1‑139 (MQ=255) aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg < 2:1165849/139‑1 (MQ=255) gATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa > 2:411018/1‑73 (MQ=255) gATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa < 1:411018/73‑1 (MQ=255) gATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAATGAATGTGTTTCAAACATTTTTTCATCTAAATAAGGTCTGGCTTGTTCGCAGATTTCGt < 2:332638/139‑1 (MQ=255) tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata < 2:1154783/70‑1 (MQ=255) tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata < 2:1380894/70‑1 (MQ=255) tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata > 1:1380894/1‑70 (MQ=255) tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCata > 1:1154783/1‑70 (MQ=255) aaaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa > 1:783167/1‑56 (MQ=255) aaaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa < 2:783167/56‑1 (MQ=255) aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa > 1:1495171/1‑62 (MQ=255) aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa < 2:1495171/62‑1 (MQ=255) aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCa > 2:1197057/1‑139 (MQ=255) aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAg < 2:51711/139‑1 (MQ=255) aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc < 1:349422/41‑1 (MQ=255) aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc > 2:349422/1‑41 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAc > 1:1555449/1‑119 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAc < 2:1555449/119‑1 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg < 2:687451/130‑1 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg > 1:687451/1‑130 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttt < 2:1043857/76‑1 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttt > 1:1043857/1‑76 (MQ=255) ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAg < 2:607354/120‑1 (MQ=255) ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAg > 1:607354/1‑120 (MQ=255) | TGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGG > NC_000913/2995183‑2995432 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |