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 |
|---|---|---|---|---|---|---|
| A12 F1 I1 R1 | 760 | 58.2 | 3022526 | 90.8% | 2744453 | 102.0 |
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% | 85.5 / NA | 28 | 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 (14/14); total (14/14) | |||||||||||
AATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGG > NC_000913/2995197‑2995432 | aaTATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGGTGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc < 2:1081684/139‑1 (MQ=255) aatTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa < 1:1222622/139‑1 (MQ=255) acaGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAc > 2:344873/1‑139 (MQ=255) aTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAttttt > 2:250617/1‑139 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa > 2:520491/1‑49 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa < 1:520491/49‑1 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAAc < 1:1166506/115‑1 (MQ=255) tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAAc > 2:1166506/1‑115 (MQ=255) aaaTCATTGAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa > 1:979920/1‑56 (MQ=255) aaaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa < 2:979920/56‑1 (MQ=255) aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCa > 1:168840/1‑82 (MQ=255) aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCa < 2:168840/82‑1 (MQ=255) aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg > 1:245/1‑139 (MQ=255) aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg < 2:245/139‑1 (MQ=255) tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt > 1:467363/1‑54 (MQ=255) tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt < 2:467363/54‑1 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt < 1:885730/47‑1 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCa > 1:409525/1‑55 (MQ=255) gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCa < 2:409525/55‑1 (MQ=255) gAGCCAGGGAGTTATAAGTCATCAGGGCTTGCCAAAACAGAattatt > 2:885730/1‑47 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATGC‑AAGAATGTGTTTCAAACATTTTTTCAACt < 1:1074915/82‑1 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt > 1:512849/1‑60 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt < 2:512849/60‑1 (MQ=255) aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCC‑AAGAATGTGTTTCAAACATTTTTTCAACt > 2:1074915/1‑82 (MQ=255) gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt > 2:712166/1‑73 (MQ=255) gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt < 1:712166/73‑1 (MQ=255) ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAGCTTGTCAg < 1:979492/120‑1 (MQ=255) ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTACGCAGATTTCGTTAACCTTGTCAg > 2:979492/1‑120 (MQ=255) | AATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGG > NC_000913/2995197‑2995432 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |