| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,669,465 | 0 | C | A | 46.0% | 69.9 / 29.4 | 50 | L240F (TTG→TTT) | yphD | ABC transporter permease |
| Reads supporting (aligned to +/- strand): ref base C (22/5); new base A (0/23); total (22/28) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 9.87e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCG > NZ_CP009273/2669380‑2669550 | tACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACaaaa > 1:2087147/1‑90 (MQ=255) cgccgACCACGACCGCGGCGATGCCGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGc < 2:2105663/90‑1 (MQ=255) cgccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGc < 1:1587017/90‑1 (MQ=255) gccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGcc > 1:1749549/1‑90 (MQ=255) gccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGcc > 2:1334938/1‑90 (MQ=255) gccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGcc > 1:3316691/1‑90 (MQ=255) gACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGt > 2:96890/1‑90 (MQ=255) gACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGt > 2:661132/1‑90 (MQ=255) ccACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCa > 1:1953234/1‑90 (MQ=255) ccgcccGCGGCGATGACGCAAACCCCCACCCCTTTGGCGCCCCCCCCGTTCCCAAACCCGGGGCCCCCCGCAAAAAAAATGCCGGTCAcc < 2:1514440/86‑1 (MQ=255) gcgAGGACGACAACCCCCAGCCCTTTGGCGGCCCCTGCGTTACCAAACCCGGGGCGCCCCCCCAAAAAAATGCCGGTCACCGCCGCtaat < 2:783571/90‑1 (MQ=255) tCAACCCCCAGACCGTTGGCGCCCCCTGCGTTCCCAGACCGGGGGCGCGCCGCAAAAAAAAGCCCGGTCACCGCCGCTAATAATCCCGaa < 2:316711/90‑1 (MQ=255) acAAACCCCACCCCGTTCGCGCCCCCTGCGTTACCAAACCCGAGGCGCGCCGCAAACAAAAGGCCGGTCACCGCCGCTAATAATCCCGaa < 2:778851/89‑1 (MQ=255) aaaaCCCCAGCCCTTTTGCGCCCCCTGCGTTCCCAGACCCGGGGCGCGCCCCCAACAAAATGCCGGTCCCCGCCGCTAATAATCCCGaaa < 1:3336378/89‑1 (MQ=255) aaccTCCAAACGGTTGGCGGCCCCTGCGTTACCAGAACCGAGGCGCGCCCCAAAAAAAATGCCGGTCCCCGCCGCTAATAATCCCGAAAg < 2:1501790/87‑1 (MQ=255) ccccgACGGTTGGCGGCCCCTGCGTCACAAAACCCGGGGCGCGCCCAAAAAAAAAGGCCGGTCCCCGCCGCTAATAATCCCGAAAGGGTa < 2:328993/86‑1 (MQ=255) cccAGCCCTTTTGCGCCCCCTGCGTTCCCAAAACCGGGGCGCCCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa < 1:2092453/89‑1 (MQ=255) cccAGCCCTTTTGCGCCACCTGGGTTCCCAGACCCGGGGCGCGCCGCCAAAAAAATGCCGGTCCCCGCCGCTAATAATCCCGAAAGGGTa < 1:1144884/89‑1 (MQ=255) cccAGCCCTTTGGCGGCCCCTGCTTTCCCAGAACCGAGGCGCGCCGCCAAAAAAATGCCGGCCACCGCCGCTAATAATCCCGAAAGGGTa < 1:331119/89‑1 (MQ=255) cccAGCCCTTTGGCGGCCCCTGCGTTACCAAAACCGGGGCGCGCCCCAAAAAAAATGCCGGTCCCCGCCGCTAATAATCCCGAAAGGGTa < 2:2087147/89‑1 (MQ=255) cccAGCCCTTTGGCGCCCCCGGCGTCCCCAAACCCGGGGGGCGCCACAAAAAAAATGCCGGCCCCCGCCGCTAACAATCCCGAAAGGGTa < 2:2743171/89‑1 (MQ=255) cccAGCCCGTTTGCGGCCCCTGCTTTCCAAAAACCGGGGCGCCCCCCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa < 2:2971600/89‑1 (MQ=255) cccAGCCCGTTGGCGCCCCCTGCTTTCCCAAAACCGGGGGGCGCCCCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa < 1:448579/89‑1 (MQ=255) cccAGACTGTTTGGGGCACCTGCGTTACCAAACCCGAGGCGCGCCCCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa < 2:1931912/89‑1 (MQ=255) cccAGACCGTTGGCGCCCCCTCCGTTACCAAACCCGGGGCGCGCCGCAAAAAAAATGCCGTTCCCCGCCGCTAATAATCCCGAAAGGGTa < 2:1768663/89‑1 (MQ=255) cccACACCGTTCGCGGCACCTGCGTTACCAAAACCGGGGCGCGCCGCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa < 2:2252871/89‑1 (MQ=255) ccAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa > 1:1146354/1‑90 (MQ=255) ccAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa > 1:697027/1‑90 (MQ=255) ccAGACCGTTGGCGCCACCTGCGTTCCCAAAACCGGGGCGCCCCCCAAAAAAAAGGCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTaa < 2:272416/90‑1 (MQ=255) cAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGTGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaaa > 2:466133/1‑90 (MQ=255) cAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaaa > 1:1931912/1‑90 (MQ=255) cAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaaa > 1:46114/1‑90 (MQ=255) cccGTTGGCGGCCCCTGCGTTCCAAAACCCGAGGCGCGCCACCAAAAAAGTGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGAt < 1:3341735/89‑1 (MQ=255) gTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAg > 2:1611151/1‑90 (MQ=255) tttGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGaa > 2:470073/1‑75 (MQ=255) tttGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGa > 2:694902/1‑90 (MQ=255) tttGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGaa < 1:470073/75‑1 (MQ=255) cACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATgcgcc > 2:1538970/1‑89 (MQ=255) ttACAAGAACCGGGGGGCGCCCCCAAAAAAATGCCGGTCTCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcgacga < 1:3090863/90‑1 (MQ=255) aGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGaa > 1:2079137/1‑55 (MQ=255) aGAACCGAGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGaa < 2:2079137/55‑1 (MQ=255) ccggAGGCGCCCCCCCAACAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGAt < 1:96890/87‑1 (MQ=255) aCCGGGGCGCCCCCCCAAAAAAATGCCGGACACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGAt < 1:3119931/90‑1 (MQ=255) gAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGcc > 2:865354/1‑90 (MQ=255) gAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGcc > 1:2719200/1‑90 (MQ=255) aGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCg > 2:1665548/1‑90 (MQ=255) gcgcCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaaa > 2:1931383/1‑52 (MQ=255) gcgcCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGcaca > 2:1723486/1‑90 (MQ=255) gcgcCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaaa < 1:1931383/52‑1 (MQ=255) ccAAAAAAACGCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAACGCGCACCCGACGAACGTTGATGCCGCACAACTgcg < 2:1980822/90‑1 (MQ=255) | TACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCG > NZ_CP009273/2669380‑2669550 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |