| 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 | 77.1% | 72.9 / 13.0 | 35 | Y240D (TAC→GAC) | lptD | LPS assembly protein LptD |
| Reads supporting (aligned to +/- strand): ref base A (5/3); new base C (12/15); total (17/18) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.43e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01 | |||||||||||
GCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTAT > NZ_CP009273/56306‑56475 | gCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt < 2:724403/90‑1 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 2:87238/90‑1 (MQ=255) gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg < 1:238655/90‑1 (MQ=255) gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg < 2:351286/90‑1 (MQ=255) gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg < 1:29288/90‑1 (MQ=255) ataATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACtt < 2:144373/90‑1 (MQ=255) aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGc > 1:282368/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCg > 1:134341/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAAACGTTGGTGGGGGTGGACTTGGGGGTCg > 2:478856/1‑90 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGGGGGGGGGGACTTTGCGGTCg > 2:552646/1‑90 (MQ=255) cgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACCCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCgg > 2:339013/1‑90 (MQ=255) tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCgaga < 2:653812/90‑1 (MQ=255) tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGa < 2:806669/90‑1 (MQ=255) aTGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTCGTTGGGGGGGGGGGACTTTggggtcggggtc > 2:325192/1‑90 (MQ=255) ccATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGGGGGGGGGGACTTGGGGTTCGGGGTCAAGAAACCag > 1:370318/1‑90 (MQ=255) tatTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGc < 2:194568/90‑1 (MQ=255) tGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGGGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACg > 1:762565/1‑90 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGc > 1:805506/1‑84 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGc < 2:805506/84‑1 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAAGAGTTGGGGGGGGGGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGtt > 2:152100/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:325192/90‑1 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:478856/90‑1 (MQ=255) atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa < 1:794569/90‑1 (MQ=255) tatGGCAGGTAGAACTCAAAGTAGTTGGGGGGGGGGTACTTGGCGTTCGGGGGCAAGAAAACAGAGCGACGTTTGTCACCCACCGGCAAc > 2:532489/1‑90 (MQ=255) tGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTg > 1:349407/1‑90 (MQ=255) gCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCa > 1:249655/1‑90 (MQ=255) aGGGAGAACTCAAAGTCGTTGGGGGTGGGGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa > 2:552238/1‑90 (MQ=255) tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 2:385463/90‑1 (MQ=255) tAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 1:532489/90‑1 (MQ=255) tAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGACGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 2:319855/90‑1 (MQ=255) tAGAACTCAAAATCGTTGGTGGGGGGGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg > 1:269509/1‑90 (MQ=255) aCTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc < 1:249117/90‑1 (MQ=255) cAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtat > 1:546300/1‑90 (MQ=255) aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg > 2:754025/1‑81 (MQ=255) aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg < 1:754025/81‑1 (MQ=255) | GCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTAT > NZ_CP009273/56306‑56475 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |