| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,549,564 | 0 | A | C | 56.0% | 12.5 / 27.8 | 25 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| Reads supporting (aligned to +/- strand): ref base A (10/1); new base C (0/14); total (10/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.37e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.79e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCAC > NZ_CP009273/3549482‑3549644 | cACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCg > 1:469742/1‑90 (MQ=255) cTTTCGACTCCAAGCGAGACGTTATTCCCCGCCCCCTGGTCGCGCGGCAGGTTATGATTATTTTGTTCATGCAGGGAAAAC‑CTCCCCGcc < 1:529930/90‑1 (MQ=255) cGAGACGGTATTCCCCGGCCCCTGGTCGCGCGGCAGTTTATGAATATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTc < 1:180123/90‑1 (MQ=255) gaCGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACg > 1:554448/1‑90 (MQ=255) aCGTTATTCCCCGCCCCCTGGCCGCGCGGCGGTTTATAAATATTTTTTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGc < 2:672686/90‑1 (MQ=255) gttATTCCCCGCCCCCTGGCCGCGGGGGGGTTTATAAATTTTTTGTTCATG‑AGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTc < 2:482397/88‑1 (MQ=255) ccGCCCCCGGGTCGCGCGGCGGGTTATGAATTTTCTGTCCAGGCGGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAt < 1:512319/90‑1 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc > 2:146253/1‑90 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc > 2:512319/1‑90 (MQ=255) gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc > 1:548758/1‑90 (MQ=255) cccGGGTCGCGCGGCGGTTTATGATTTTTTTTTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgcgc < 2:548758/90‑1 (MQ=255) cgcgcgGAAGTTTATAAATTTTCTTTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac < 2:469742/90‑1 (MQ=255) cgcgcgGAAGTTTATAAATTTTCTGTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac < 1:736936/90‑1 (MQ=255) gcgcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCGGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACAcc > 1:528979/1‑90 (MQ=255) gcggcgGTTTATAAATTTTCTGTTCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAg < 1:424867/90‑1 (MQ=255) cAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTaa > 2:103725/1‑90 (MQ=255) aaTTTTCTGTTCATGGAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc < 1:608049/90‑1 (MQ=255) ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa > 2:523672/1‑90 (MQ=255) tCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc < 1:167983/90‑1 (MQ=255) tCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc < 1:270702/90‑1 (MQ=255) tCTGTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc < 2:398316/90‑1 (MQ=255) tGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCCCCACGc > 1:619418/1‑90 (MQ=255) gTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCa > 1:586752/1‑90 (MQ=255) cAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac < 1:538058/90‑1 (MQ=255) cAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac < 1:146253/90‑1 (MQ=255) | CACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCAC > NZ_CP009273/3549482‑3549644 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |