| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,860,603 | 0 | A | T | 64.7% | ‑4.8 / 27.7 | 34 | V103E (GTA→GAA) | rpoS | RNA polymerase sigma factor RpoS |
| Reads supporting (aligned to +/- strand): ref base A (2/10); new base T (22/0); total (24/10) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.03e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-05 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTC > NZ_CP009273/2860519‑2860691 | aCCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTaccacc < 2:758675/90‑1 (MQ=255) ccGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAAATTTTTccccca > 1:431599/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTtccccccaa > 1:342000/1‑87 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTTCCACCCGa > 2:134912/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTtccacccaa > 1:550608/1‑87 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGa > 2:558857/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGa > 2:51324/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGa > 2:622811/1‑90 (MQ=255) gcgcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGa > 2:699969/1‑90 (MQ=255) gcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACg > 2:656073/1‑90 (MQ=255) gcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACg < 1:51324/90‑1 (MQ=255) gcgGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACg < 2:666908/90‑1 (MQ=255) tCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGt < 1:230581/90‑1 (MQ=255) tCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGt < 1:897590/90‑1 (MQ=255) cccAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTActc < 2:610042/90‑1 (MQ=255) ccAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAATTTTTCCACCAGACGCCAATTActct > 1:188352/1‑90 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCCCCCAACGCAAGTTACTCTCg > 2:755076/1‑90 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAAACGCAAGTTTCTCTCg > 2:397092/1‑90 (MQ=255) aGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAAACGCAAAGTACTCTCg > 1:387400/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTTCCCCCACACGCAAGTTAATTTCcatcat > 1:254283/1‑90 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGtt > 2:562881/1‑78 (MQ=255) gCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGtt < 1:562881/78‑1 (MQ=255) ctTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTACCCCCAGACGCAAGTTACTCTCGGTCATcccgg > 2:252547/1‑87 (MQ=255) ctTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTATTCTCCATCATCcggc > 2:294113/1‑90 (MQ=255) ctTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCGGTCATCccgc > 2:15098/1‑90 (MQ=255) ctTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCGATCATCcggc > 2:73969/1‑90 (MQ=255) ctTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAACTTTTTCCACCCAACGCAAGTTAGCCCCCCTCATCcggc > 2:242842/1‑90 (MQ=255) ttCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTTTCACCAAACGCAAAGTACTCTCGATCATCcggcg > 1:763480/1‑90 (MQ=255) aGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCGACGCAAGGTACTCTCGATCATCCGGCGGGGggag > 1:269350/1‑90 (MQ=255) gTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCGACGCAAGTTACTCTCGATCATCCGGCGGCGGGAggg > 2:152732/1‑89 (MQ=255) ccAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAATTTTTTCACCCAACCCCAATTACTCTCCATCAACCCGCGGCGGGAGGCGa > 1:872608/1‑90 (MQ=255) cAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGAc < 2:872608/90‑1 (MQ=255) gCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCGACGCAAGTTACTCTCCATCATCCGGCGGCGAGAGGGGAAATCTccc > 2:474868/1‑89 (MQ=255) aGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGc < 1:656073/90‑1 (MQ=255) tGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCCCGCAGGGCGCGAc > 2:583196/1‑90 (MQ=255) aTTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAActtct < 2:39633/90‑1 (MQ=255) tACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGTGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACttcttcttc < 2:170096/90‑1 (MQ=255) | ACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTC > NZ_CP009273/2860519‑2860691 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |