| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 56,379 | 0 | T | G | 53.8% | 10.2 / 23.3 | 26 | Y244S (TAC→TCC) | lptD | LPS assembly protein LptD |
| Reads supporting (aligned to +/- strand): ref base T (6/6); new base G (14/0); total (20/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.01e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.88e-02 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TCCCACATGATGTTGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAA > NZ_CP009273/56292‑56465 | tcCCACATGATGTTGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAg > 2:318682/1‑90 (MQ=255) gTTGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCaaaaaa > 1:53775/1‑87 (MQ=255) ccACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTAGTtg > 2:44740/1‑90 (MQ=255) acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTtggt < 2:48312/90‑1 (MQ=255) aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTAGTTGGTGGGGGGGTACTTggg > 2:351743/1‑89 (MQ=255) aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTAGTTGGTGGGGGGGGAATTGGc > 2:13046/1‑90 (MQ=255) tGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGGAATCAAAAAAGGTGGGGGGGGGGTACTTGGCg > 1:608254/1‑90 (MQ=255) gcggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAATAATATGGCAGGGAGAACTCAAAGTAGTTGGTGGGGGGGGACTTTGCGt > 2:144926/1‑90 (MQ=255) cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAAATCAAAGTAGTTGGGGGGGGGGTACTTTGCGtt > 2:370168/1‑90 (MQ=255) cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGGGAAATCAAAGTAATTTGGGGTGGGGGACTTGGCGtt > 1:530829/1‑90 (MQ=255) cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATAGTTTGGGGGGGGGTACTTGGGGtt > 1:372730/1‑90 (MQ=255) cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAAGAGTTGGGGGGGGGGTACTTTGCGtt > 1:476900/1‑90 (MQ=255) ggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTc < 1:349395/90‑1 (MQ=255) gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATAGTTGGGGGGGGGGTAGTTGGCGTTCg > 1:324591/1‑90 (MQ=255) ggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGaa < 1:136807/90‑1 (MQ=255) gcgcGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTAGTTGGGGGTGGTGTACTTTGGGTTCGGGATCAAGAAACCAGAacgacggt > 1:471192/1‑88 (MQ=255) cgcgATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTAGTTGGTGGGGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGgtt > 2:195047/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa < 1:243209/90‑1 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa > 2:491997/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGGGTACTTGGCGTTCGGGGTCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa > 2:38890/1‑90 (MQ=255) aaTATGGCAGGTAGAACTCAAAGTAGTTGGGGGGGGGGTACTTGGCGTTCGGGGTCAAAAAACCAGAGCGACGGTTGTCACCCACCGGCa > 1:527186/1‑90 (MQ=255) atatGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa < 1:464823/90‑1 (MQ=255) tatGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAAcc < 1:572234/62‑1 (MQ=255) tatGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAAcc > 2:572234/1‑62 (MQ=255) aGGTAGAACTCAAAGTAGTTGGGGGTGGGGTACTTGGCGGTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCCCCGGCAACTGCaaa > 2:573998/1‑90 (MQ=255) aGGGAGAACTCAAAGTAGTTGGGGGGGGGGTACTTGGCGTTCGGGGTCAAGAAAACAGAGCGACGGTTGTCACCCACCGGCAACTGCaaa > 1:577399/1‑90 (MQ=255) | TCCCACATGATGTTGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAA > NZ_CP009273/56292‑56465 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |