| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NZ_CP009273 | 56,392 | A→C | Y240D (TAC→GAC) | lptD ← | LPS assembly protein LptD |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 56,392 | 0 | A | C | 97.1% | 190.2 / ‑3.9 | 69 | Y240D (TAC→GAC) | lptD | LPS assembly protein LptD |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (39/28); total (40/29) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.20e-01 | |||||||||||
TGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA > NZ_CP009273/56305‑56477 | tGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAagtcgt > 1:1112267/1‑90 (MQ=255) gCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt < 1:1260210/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 2:74806/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 2:368930/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 2:270446/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 2:1095256/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 1:879461/90‑1 (MQ=255) gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtgg > 2:946093/1‑90 (MQ=255) gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGGACTCAAAAACGTtggtgg > 1:1186758/1‑90 (MQ=255) gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTtggtgg > 2:985628/1‑90 (MQ=255) cgaTGCATATAACGCGGAGTGAAGGTGGCATCCATACTTGGCGCGATATTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtg < 1:1059951/90‑1 (MQ=255) gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg < 1:186502/90‑1 (MQ=255) gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg < 1:886795/90‑1 (MQ=255) aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTggtggtggt < 2:433456/90‑1 (MQ=255) aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTggtggtggt < 2:156737/90‑1 (MQ=255) aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAATCGTtggtggtggg > 2:903934/1‑89 (MQ=255) aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTtggggggggg > 1:207814/1‑89 (MQ=255) tGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGgtggtggtg < 2:1130089/90‑1 (MQ=255) taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTg > 1:582390/1‑90 (MQ=255) aaTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTgg < 1:985628/90‑1 (MQ=255) ggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAAACGTTGGGGGGGGGGTACTTTGCggtt > 1:1519566/1‑87 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGGTCg > 2:1550645/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGGACTTGGGGGTCg > 2:694045/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGTGGGGGACTTTGGGtttg > 1:310319/1‑88 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTGGGGtttg > 1:364168/1‑88 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTAGTTGGGGGGGGGGTACTTGGCGGTCg > 1:117479/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGTACTTTGCGTTCg > 1:1409582/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGTACTTGGGGGTCg > 2:1309631/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAAGCGTTGGGGGGGGGGGACTTTGCGGTCg > 1:877430/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGGCGTTGGTGGGGGGGGACTTGGCGGTCg > 2:1132634/1‑90 (MQ=255) tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCCTTCGGGa < 1:1529740/90‑1 (MQ=255) aTGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATc < 1:1401037/90‑1 (MQ=255) gtggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAg < 1:9887/90‑1 (MQ=255) aTCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCGGGATCAAGAAAcc > 2:485591/1‑90 (MQ=255) tGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACg > 2:385992/1‑90 (MQ=255) tGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACg > 2:15310/1‑90 (MQ=255) ggCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGGCGTTGGGGGTGGGGTACTTGGCGTTCGGGATCAAGAAAACAGAGCGACGt > 2:843825/1‑90 (MQ=255) ggCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGTGTACTTGGCGTTTGGGGTCAAGAAACCAGAGCGACGt > 1:263114/1‑90 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTTGTGGGGGTGTACTTTGCGTTTGGGATCAAGAAACCAGAGCGACGtt > 2:1194048/1‑90 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTGGCGTTCGGGGTCAAGAAACCAGAGCGACGtt > 2:951052/1‑90 (MQ=255) cgATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGGGGGGGGGTACTTGGGGGTTGGGGTCAAGAAACCAAAGCGACGTTTGt > 1:1227838/1‑90 (MQ=255) gATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCGGGGTCAAGAAACCAGAGCGACGTTTGTc > 1:601543/1‑90 (MQ=255) gATGTTCCAGTAATATGGCAGGGAGAACTCAAAGACGTTGGGGGGGGGGTAATTGGCGTTCGGGGTCAAGAAACCAGAGGGAAGGTTGtg > 1:906512/1‑89 (MQ=255) gTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTGGCGTTCGGGGTCAAAAAAACAAAGCGACGGTTGTCACCCACCgg > 1:1440413/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAGAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa > 2:347506/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:620244/90‑1 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:217852/90‑1 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:879695/90‑1 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa > 2:620244/1‑90 (MQ=255) atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa < 2:172677/90‑1 (MQ=255) ggCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGc > 2:182475/1‑90 (MQ=255) ggCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGc > 2:586761/1‑90 (MQ=255) ggCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGc > 1:177271/1‑90 (MQ=255) aGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa > 2:15527/1‑90 (MQ=255) aGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGGTTGTCACCCACCGGCAACTGCaaa > 2:1481825/1‑90 (MQ=255) aGGTAGAACTCAAAGTCGTTGGTGGGGGTGGACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCCCCGGCAACTGCaaa > 2:790789/1‑90 (MQ=255) aGGTAGAACTCAAAGTCGTTGGGGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa > 2:312790/1‑90 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 1:38409/90‑1 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 1:874061/90‑1 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 2:776880/90‑1 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 1:930455/90‑1 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 2:263114/90‑1 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 2:1190013/90‑1 (MQ=255) gAACTCAAAGTCGTCGGTGGTGGTGTAATTGGAGTTCGGGCCCAAGAACCCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAggg < 1:1390490/90‑1 (MQ=255) aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGc > 1:1347794/1‑74 (MQ=255) aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGc < 2:1347794/74‑1 (MQ=255) aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc > 1:926079/1‑90 (MQ=255) aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc < 1:584752/90‑1 (MQ=255) aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc > 1:38682/1‑90 (MQ=255) aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaa > 1:246146/1‑90 (MQ=255) | TGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA > NZ_CP009273/56305‑56477 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |