| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,088,058 | 0 | C | . | 52.5% | 58.5 / 90.5 | 40 | coding (382/981 nt) | yggR | type IV pilus twitching motility protein PilT |
| Reads supporting (aligned to +/- strand): ref base C (8/11); new base . (11/10); total (19/21) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.45e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.22e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTGCTGGATCAAACATCGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAATGCCATGCCGTTGCGCG > NZ_CP009273/3087924‑3088191 | ctgctgGATCAAACATCGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGccccc > 1:167054/1‑139 (MQ=255)ctgctgGATCAAACATCGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGccccc < 1:538952/139‑1 (MQ=255) aaCATCGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAAt < 2:262824/139‑1 (MQ=255) cGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGc > 1:422961/1‑138 (MQ=255) gctggcATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATtct < 2:697855/139‑1 (MQ=255) gcATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCg < 1:657965/137‑1 (MQ=255) gcATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCCTCGCCCCCGTCACCAGAATCAGGCCATTCTCg < 1:663997/138‑1 (MQ=255) agaTATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCtt > 1:765266/1‑137 (MQ=255) atatTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCg > 2:483383/1‑107 (MQ=255) atatTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCg < 1:483383/107‑1 (MQ=255) atTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAAt > 1:490563/1‑139 (MQ=255) atTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAAt > 1:518621/1‑139 (MQ=255) ttCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGa < 2:97519/134‑1 (MQ=255) ttCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGa > 1:97519/1‑134 (MQ=255) ttCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAAt > 1:141744/1‑139 (MQ=255) ttCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAAt < 1:11076/138‑1 (MQ=255) tCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCAcc < 2:740899/95‑1 (MQ=255) tCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCAcc > 1:740899/1‑95 (MQ=255) cGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTg > 2:120915/1‑139 (MQ=255) tCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTg < 1:402316/120‑1 (MQ=255) tCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTg > 2:402316/1‑120 (MQ=255) tCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAg > 1:405290/1‑139 (MQ=255) tGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCgg < 2:405290/139‑1 (MQ=255) ttgaGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGt < 2:344538/139‑1 (MQ=255) agaTAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCg < 1:735476/139‑1 (MQ=255) agaTAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCg < 2:490563/138‑1 (MQ=255) aTAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCg > 1:731631/1‑137 (MQ=255) gCCAACCAGCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATGCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTa < 1:102165/139‑1 (MQ=255) ccAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCAc < 2:166479/53‑1 (MQ=255) ccAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCAc > 1:166479/1‑53 (MQ=255) ccAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCg > 2:585055/1‑132 (MQ=255) ccAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCg < 1:585055/132‑1 (MQ=255) ccAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTaa < 2:422961/139‑1 (MQ=255) gccgccAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGt < 1:520230/138‑1 (MQ=255) tGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCTTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAatgccat < 1:571776/138‑1 (MQ=255) gCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCggg > 2:196335/1‑97 (MQ=255) gCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCggg < 1:196335/97‑1 (MQ=255) accccccGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAgtgccatg < 2:756004/132‑1 (MQ=255) aCTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAgtgccatg > 1:756004/1‑135 (MQ=255) cGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAATGCCATGCCGTTGcgcg > 1:212860/1‑138 (MQ=255) cGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAATGCCATGCCGTTGcgcg > 2:353994/1‑138 (MQ=255) cGTCG‑CCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAATGCCATGCCGTTGcgcg > 2:498538/1‑138 (MQ=255) | CTGCTGGATCAAACATCGCTGGCTGGCATAGAGATATTCAACAGGATCTTCCAGCGTCAGAATATGCGCATCGGCATGTTGATTGAGATAGCCAACCATCGCCGCCAGCGTGGTAGATTTGCCACTCCCCGTCGCCCCCGTCACCAGAATCAGGCCATTCTCGCTCTTGAGTAATTCCGGCAATACCGTTGGTGCGCCAAGCTGTTCGAGCTGCGGGCAGTGCGAAGGTAACAGCCGTAACGCCAGCGAAATGCCATGCCGTTGCGCG > NZ_CP009273/3087924‑3088191 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |