| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,995,399 | 0 | A | C | 53.8% | 5.5 / 14.4 | 13 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| Reads supporting (aligned to +/- strand): ref base A (5/1); new base C (0/7); total (5/8) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.66e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTA > NZ_CP009273/1995315‑1995481 | tttCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCccg > 1:87866/1‑90 (MQ=255) ttCTGCAGGGTTTTTAATCGGACGATGGGGGGGTAAAAGGGGGGGTTATTG‑GGGGGTTACAGGAAAATCCCAGGCAAAAAAAAACCccgc < 2:398228/90‑1 (MQ=255) gggTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAACCCCCGCCGGTGGc < 1:231077/90‑1 (MQ=255) ttaaaTCGGACGTTTGGGGGGGGAAAGGGGGGGTTTTTG‑GGGGTTTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGa < 1:517797/87‑1 (MQ=255) ggACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGt > 1:73160/1‑90 (MQ=255) ggTAAAAGGGGGGTTTTTTG‑GGGGGTTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt < 2:87866/90‑1 (MQ=255) aaaaTGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg > 1:91595/2‑90 (MQ=255) aggggggTTTTTTGGGGGGTTAAAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCtt < 2:501166/87‑1 (MQ=255) cAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc < 2:210844/90‑1 (MQ=37) aGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg > 2:416487/1‑90 (MQ=255) ggCAGAAAAAACCCCCGCCGGTGGTGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCgg < 1:170254/90‑1 (MQ=255) ggCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCgg < 2:91595/90‑1 (MQ=255) gAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGAGTAAACGCCTTATCCGGCCTa > 1:22224/1‑90 (MQ=255) | TTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTA > NZ_CP009273/1995315‑1995481 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |