| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,860,603 | 0 | A | T | 52.6% | ‑1.7 / 12.8 | 20 | V103E (GTA→GAA) | rpoS | RNA polymerase sigma factor RpoS |
| Reads supporting (aligned to +/- strand): ref base A (3/6); new base T (10/0); total (14/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.10e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.29e-02 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAA > NZ_CP009273/2860515‑2860681 | ctctACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTac > 1:33593/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGa > 1:449860/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAATTTTTTCACCAGa > 2:666594/1‑90 (MQ=255) gcgGATCAGCCCCAGGTTACCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACg > 1:661470/1‑90 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAAACGCAAGTTACTCTCg > 1:478948/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCCACGCAAGGTACTCTCGctcat > 2:126374/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTCACACCCTACGCAAGTTAGTCTTcatcat > 1:481695/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAATTTTTTCTCCCGACGCAAGTTACTCTCcatcat > 2:517635/1‑90 (MQ=255) gTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAggg > 1:429230/1‑89 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:335150/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:32239/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:160575/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 2:33593/90‑1 (MQ=255) gCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCGACGCAAGTTACTCTCGATCATCCCGCGGCGAGAGGCGACAt > 1:489595/1‑90 (MQ=255) aGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCACCCGGCGGCGAGAGGCGACATCTCCACGc < 1:402779/90‑1 (MQ=255) aCGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAATTACTCTCGATCATCCGGCGGGGAGAGGCGGCATCTCCACGCAGTgc > 2:179996/1‑90 (MQ=255) cGATTGCCATAACGGCGGGCAATTTTTTCCACCCACCCCCAGCTACTCCCGAACACCCCGCGGCGGGGGGCGACATCTCCCCCCAGGgcg > 2:402779/1‑90 (MQ=255) aaCGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCaa < 1:528625/90‑1 (MQ=255) gcggGCAATTTTTACCACCCGACGCAAGTTTCTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCCGTGCGCGACGCGCcaaaaa > 1:431128/1‑88 (MQ=255) gggCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATaaa > 1:278206/1‑90 (MQ=255) gggCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATaaa > 1:165726/1‑90 (MQ=255) | CTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAA > NZ_CP009273/2860515‑2860681 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |