| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 46.7% | 57.9 / 41.5 | 60 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (28/4); new base A (0/28); total (28/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.55e-13 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353514‑353689 | aTTTCCGCCATCAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑c‑aac‑aa > 2:1423139/1‑90 (MQ=255)aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑c‑aac‑aa > 2:3133768/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑aaa > 1:2718945/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑aaa > 1:217658/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGGCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑aaa > 2:1486348/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑ccgc > 2:2222935/1‑90 (MQ=255) ccaaacaccCGCGCTTTTATCCACCCCCGTGTGAAAAAATGCC‑TCGGCGGGGCC‑TGTCTGCCAGCTTTTTTTCCG‑CCG‑C‑AAA‑AAAC‑ccgc < 1:1802839/87‑1 (MQ=16) caacacCCGCGATTTTACCCACCGCCATGTAAAAAAATGCC‑TCCGGGGCGGC‑TGTCTGCCAGCTTTTTTCCCC‑CCG‑C‑AAA‑AAAA‑ccgccg < 1:481210/90‑1 (MQ=16) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGtt > 1:651956/1‑90 (MQ=255) cacccGCGCTTTTACCCAACGCCATGTGAAAAAATGCC‑TTCGGGGCGGC‑TGTCGGCCAGTTTTTTTCCCG‑CCG‑C‑AAA‑AAAA‑CCGCCGTtc < 1:236594/87‑1 (MQ=21) cacccGCCCTTTTACCCACCCCCTTGTGAAAAAAGGCC‑TTCGCGGGGGT‑TGTCTGCCAGTTTTTTTCCCG‑CCG‑C‑AAA‑AAAA‑CCGCCGTtc < 1:527125/87‑1 (MQ=255) caacCGCGCTTTTACCCAACCCCATGTGAAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTCCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTtc < 1:568367/90‑1 (MQ=25) aacccGCGCTTTTACCCAACCCCATGTGAAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTTTTTTCCCG‑CCG‑C‑AAA‑AAAA‑CCGCCGTtc < 1:1253197/87‑1 (MQ=21) gcgcATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTcc > 1:1034152/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTcc > 1:1089095/1‑90 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCagtag > 1:975112/1‑90 (MQ=255) tATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTg > 2:2518136/1‑90 (MQ=255) cccACCGCCATGGAAAAAAATGCT‑TTCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCC‑CCG‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:430828/89‑1 (MQ=255) cccAACCCAATGTAAAAAAATCCC‑TTCGCGGGGGC‑TGTCGGCCAGTTTTTTTCCCG‑CCG‑C‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:481803/89‑1 (MQ=255) aCGCCATGTGCAAAAATTCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1845466/1‑90 (MQ=255) aCGCCATGTGCAAAAATTCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1536223/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCATCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:2693454/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCGCGCGTGGCgggt > 2:333149/1‑89 (MQ=25) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGctgtc > 1:1182995/1‑86 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:3214234/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:3360844/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:3365264/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:952553/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:2079722/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1084383/1‑90 (MQ=255) gCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggg > 1:1448359/1‑88 (MQ=255) gCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggg > 2:3164859/1‑88 (MQ=255) ccATGTACAAAAACCCC‑TCCGGGGGGGC‑TGTCTGCCAGTTTTTTTCCCC‑CCC‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCaa < 1:740109/90‑1 (MQ=255) cttgtgAAAAAATGCC‑TCCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCG‑CCG‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAag < 1:25865/88‑1 (MQ=255) cATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggggg > 1:1092825/1‑86 (MQ=255) aTGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGaaaa > 1:2602854/1‑88 (MQ=255) tgtgCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGagag > 1:1846911/1‑90 (MQ=255) cAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaa > 1:2623508/1‑89 (MQ=38) cAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaa > 1:2311018/1‑89 (MQ=255) aaaaaaTCC‑TTCGGGGGGGGTTGTCTGCCATTTTTTTTCCCC‑CCC‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:1056546/90‑1 (MQ=255) aaaaaTGCC‑TCCGCGGGGGT‑TGTCTCCCATTTTTTTTCCCC‑CCG‑C‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:1019056/90‑1 (MQ=255) aaaaaTGCC‑TCCGCGGCGGC‑TGTCTGCCAGTTTTTTTCCCC‑CCG‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:2198907/90‑1 (MQ=37) aaaaTGCCTTTCGGGGCGGT‑TGTCTGCCAGTTTTTTTCCCG‑CCG‑C‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:632556/90‑1 (MQ=255) ttCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGAATTaaaa > 2:343489/1‑88 (MQ=255) tCGGGGCGGC‑TGTCTGCCACCTTTTTTCCCC‑CCG‑C‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:1793056/90‑1 (MQ=255) cgggggcggt‑TTTCTGCCAGTTTTTTTCCCC‑CCC‑A‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:1356869/86‑1 (MQ=255) cgggggC‑TGTCCCCCAGTTTTTTTCCCG‑CCA‑A‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt < 2:133525/90‑1 (MQ=255) tttttttcCCG‑CCG‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:2104109/87‑1 (MQ=255) tttttttcCCC‑CCG‑A‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:312902/87‑1 (MQ=255) tttttttCCC‑CCC‑A‑AAA‑AAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:3175990/88‑1 (MQ=255) cttttttCCC‑CCC‑C‑AAA‑AAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:2580012/88‑1 (MQ=255) tttttcCCG‑CCG‑C‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:2286907/89‑1 (MQ=255) tttttcCCG‑CCC‑C‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:2978824/89‑1 (MQ=255) tttttCCGCCCA‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:620263/90‑1 (MQ=255) tttttCCG‑GCACC‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1845466/90‑1 (MQ=255) tttttCCC‑CCC‑CAAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1469776/90‑1 (MQ=255) tttttCCC‑CCC‑A‑AAA‑AAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1846911/90‑1 (MQ=255) ttccccg‑cca‑A‑AAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:2856479/86‑1 (MQ=255) tccccg‑ccc‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc < 1:1867808/87‑1 (MQ=255) tCCG‑CCC‑C‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 1:2029405/90‑1 (MQ=255) g‑ccg‑a‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:2105761/90‑1 (MQ=255) cccg‑a‑AAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:3164859/89‑1 (MQ=255) aac‑aaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt < 2:2079722/90‑1 (MQ=255) ac‑aaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg < 2:131971/90‑1 (MQ=255) | ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCG‑CCG‑C‑AAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353514‑353689 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |