| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,860,603 | 0 | A | T | 35.5% | 36.5 / 10.5 | 31 | V103E (GTA→GAA) | rpoS | RNA polymerase sigma factor RpoS |
| Reads supporting (aligned to +/- strand): ref base A (3/17); new base T (11/0); total (14/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.30e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAA > NZ_CP009273/2860522‑2860681 | gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAAATTTTTCCACCCGa > 2:282034/1‑90 (MQ=255)gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTtcaccaca > 2:188/1‑88 (MQ=255)gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTTCACCAGa > 1:541507/1‑90 (MQ=255) cgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGc < 1:27983/90‑1 (MQ=255) cgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGc < 1:340343/90‑1 (MQ=255) tCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGt > 1:93481/1‑90 (MQ=255) tCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGt < 1:119016/90‑1 (MQ=255) tCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGt < 1:197059/90‑1 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCCACGCAAATTACTCTCg > 2:126571/1‑90 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCg > 1:361084/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTccacca > 2:543259/1‑68 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTAccacca < 1:543259/68‑1 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGatcat > 2:203520/1‑90 (MQ=255) gTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGc > 1:606237/1‑90 (MQ=255) gTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAATTTTTTCACCAAACGCAAGTTACTCTCGCTCATCCCGCGGCGGGAggg > 2:392914/1‑89 (MQ=255) tCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCg < 1:188/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 2:93481/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:5247/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:418727/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:282034/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:203520/90‑1 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 1:126571/90‑1 (MQ=255) gCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAt < 1:410015/90‑1 (MQ=255) gCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAt < 2:361084/90‑1 (MQ=255) cGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTTCCACCCAACGCAAGTTACTCTCCATCATCCGGCGGCGAGGGGGGACATCTcc > 2:432835/1‑90 (MQ=255) cGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTtccac > 1:531845/1‑42 (MQ=255) cGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTaccac < 2:531845/42‑1 (MQ=255) gCCAGACCACGATTGCCATAACGGCGGGTAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCa < 1:203310/90‑1 (MQ=255) gCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCa < 2:26230/80‑1 (MQ=255) gCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCa > 1:26230/1‑80 (MQ=255) cggGCAATTTTTACCCCCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATaa < 2:541507/90‑1 (MQ=255) gggCAATTTTTTCCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGGGAGGCGGCATCTCCCCGCAGTGCGCGACGCGCaaaaaaaa > 2:396461/1‑90 (MQ=255) gggCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGGGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATaaa > 1:589407/1‑90 (MQ=255) | GCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAA > NZ_CP009273/2860522‑2860681 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |