| 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 | 94.1% | 36.9 / ‑3.2 | 17 | Y240D (TAC→GAC) | lptD | LPS assembly protein LptD |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (10/6); total (10/7) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.12e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.79e-01 | |||||||||||
ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAAA > NZ_CP009273/56309‑56478 | acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt < 1:270438/90‑1 (MQ=255) gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtgg < 1:349926/90‑1 (MQ=255) aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTggtgggggt > 2:43470/1‑90 (MQ=255) aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGc > 2:236864/1‑90 (MQ=255) cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGTACTTGGCGtt > 2:428885/1‑90 (MQ=255) ggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTc < 2:373787/90‑1 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGACGGTGGGGGGGGGGGTCTTGGGGTTCg > 1:314810/1‑90 (MQ=255) tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGa < 2:512965/90‑1 (MQ=255) gATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGGGAACTCCAAAGCGTTGGGGGGGGGGTACTTTGGGGTCggggt > 1:543245/1‑88 (MQ=255) tggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt < 2:486424/58‑1 (MQ=255) tggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGtt > 1:486424/1‑58 (MQ=255) ggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCGGGATCAAGaa > 2:109413/1‑90 (MQ=255) ccATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGGACTCAAAAGCGTTGGTGGTGGTGTTCTTGGCGTTCGGGGGCAAGAAACCaa > 1:412347/1‑89 (MQ=255) tAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGc < 2:430782/90‑1 (MQ=255) aaTATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGGACTTGGCGTTCGGGGTCAAGAAACCAAAGCGACGGTTGTCACCCACCGGcc > 1:284755/1‑89 (MQ=255) atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa < 1:102845/90‑1 (MQ=255) tGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTg > 2:345765/1‑90 (MQ=255) agtcgtTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaaa < 2:183563/90‑1 (MQ=255) | ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAAA > NZ_CP009273/56309‑56478 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |