| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,549,566 | 0 | T | C | 41.4% | 38.3 / 12.3 | 29 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| Reads supporting (aligned to +/- strand): ref base T (17/0); new base C (0/12); total (17/12) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.93e-08 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAAT > NZ_CP009273/3549486‑3549647 | ttCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAg > 2:769114/1‑90 (MQ=255)ttCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAg > 2:72933/1‑90 (MQ=255) tCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAgt > 1:46609/1‑90 (MQ=255) cAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGa > 2:195972/1‑90 (MQ=255) cagttATTCCCCGGCCCCTGGGCGCGCGGCAGGTTATAAATTTTTTGTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGc < 2:919688/86‑1 (MQ=255) ggTCTTCCCCGCCCCTTGGCCGCGCGGAAGTTTATAAATTTTCTGTTCAGGAAGGAAAACC‑CCCCCCGCCAGTGTAGCGATTTCACGCTc < 1:465237/90‑1 (MQ=255) aCCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAAc > 1:336210/1‑90 (MQ=255) ggCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAtct > 1:867628/1‑88 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAtctg > 1:919688/1‑87 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAtctg > 2:807736/1‑87 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc > 2:400319/1‑90 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc > 1:396957/1‑90 (MQ=255) gccgcgcgGCGGTTTATGAATTTTCTTTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcac < 1:195972/88‑1 (MQ=255) cgcgcgGCGGTTTATAAATTTTTTTTTCA‑GGAGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac < 2:336210/90‑1 (MQ=255) ttATAAATTTTCTTTTCAGGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGa < 2:396957/90‑1 (MQ=255) aaTTTTCTTTTCAGGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc < 1:769114/90‑1 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCAc > 2:341464/1‑46 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa > 2:344538/1‑90 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa > 2:329461/1‑90 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa > 1:837906/1‑90 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CCCCCCGCCAGTGTAGCGATTTCAc < 1:341464/46‑1 (MQ=255) tCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc < 1:242636/90‑1 (MQ=255) tGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGc > 2:865197/1‑90 (MQ=255) aTGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg > 1:245629/1‑90 (MQ=255) tGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCgg > 2:388360/1‑56 (MQ=255) tGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCgg < 1:388360/56‑1 (MQ=255) gaGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac < 2:46609/89‑1 (MQ=255) ggaaaaac‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACaa < 1:72933/87‑1 (MQ=255) gaaaaac‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAAt < 1:400319/88‑1 (MQ=255) | TTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAAT > NZ_CP009273/3549486‑3549647 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |