| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,591 | 0 | T | C | 58.1% | 21.4 / 40.6 | 31 | K271E (AAA→GAA) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base T (11/2); new base C (0/18); total (11/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 9.21e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.59e-06 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTG > NZ_CP009273/353502‑353677 | cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTAttttt > 2:880931/1‑90 (MQ=255)cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTAttttt > 1:390219/1‑90 (MQ=255)cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTAttttt > 2:763435/1‑90 (MQ=255)cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTAttttt > 2:23864/1‑90 (MQ=255)cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTAttttt > 2:186268/1‑90 (MQ=255) gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTccgcc < 2:689755/90‑1 (MQ=255) aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGca > 2:15065/1‑90 (MQ=255) ttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa > 1:26133/1‑90 (MQ=255) ccGCAAACACCCGCCCATTTATCCACCCCCATGTGCAAAAACGCTTC‑CGCGGC‑GGCTGTCTGCCCGATTTTTTCCCGCCGCAACAAAG‑‑cc < 2:221333/90‑1 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑ccgc > 2:112471/1‑90 (MQ=255) cagccGCGCTTTTACCCACCCCCATGTGCAAAAATCCCTT‑CGGGGG‑GGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAA‑‑CCGCCGTtc < 2:789221/87‑1 (MQ=21) cacccGCGTTTTTACCCACCCCCATGTGAAAAAATCCCTT‑CGGGGC‑GGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTtc < 2:364560/87‑1 (MQ=16) cacccGCGTTTTTACCCACCCCCATGTAAAAAAATGCCTT‑CGGGGC‑GGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTtc < 2:751823/87‑1 (MQ=16) cacccGCGTTTTTACCAACCGCCATGTGAAAAATTCCCTT‑CGGGGG‑GGCTGTCTCCCAGTTTTTTTCCCGCCGCAACAAAA‑‑CCGCCGTtc < 2:361212/87‑1 (MQ=255) cacccGCGCTTTTATCCAACGCCATGTGAAAAAATGCCTT‑CGCGGG‑GGCTGTCGGCCAGTTTTTTTCCCGCCGAAACAAAA‑‑CCGCCGTtc < 2:706271/87‑1 (MQ=21) caacCGCGCATTTACCCAACCCCATGTGAAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTtc < 2:136165/90‑1 (MQ=21) ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTtctct > 1:849809/1‑90 (MQ=255) ccGCGATTTTACCCACCCCCATGTGAAAAAAGCCCTT‑CGGGGG‑GGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTtctct < 2:402763/90‑1 (MQ=255) gcgcTTTTACCCACCGCCATGTGAAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAA‑‑CCGCCGTTCTCTcc < 2:26133/90‑1 (MQ=25) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTcc > 2:317479/1‑90 (MQ=255) aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTgg > 1:79586/1‑90 (MQ=255) ccaccATGTCAAAAAATGCCTC‑CGGGGC‑GGTTTCCTCCCGGCTTTTTTCCCCCCAAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCgggg < 2:493122/87‑1 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGcctgt > 1:584720/1‑86 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:271343/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:622331/1‑90 (MQ=255) aTGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAaga > 2:880831/1‑90 (MQ=255) aTGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCCaga > 2:823344/1‑90 (MQ=255) cAAAAAGCCCTC‑CGGGGC‑GGCTGTCGCCCATTTTTTTTCCCGCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:16884/90‑1 (MQ=255) aaaaaTGCTTT‑CGGGGG‑GGTTGTCGGCCGGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:441221/90‑1 (MQ=255) aaaaaTGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:53291/90‑1 (MQ=38) aaaaaTGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGGCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:437405/90‑1 (MQ=255) aaaaaTCCCTTCCGCGGC‑GCCTGTCGGCCATTTTTTTTCCCCCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:625053/90‑1 (MQ=255) aaaaaTCCCCT‑CGGGGGGGGCTGTCGGCCGTTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:14392/90‑1 (MQ=255) t‑CGCGGC‑GGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:79586/90‑1 (MQ=255) cggcggc‑gGCTTTCTCCCTTTTTTTTCCCCGCCAAAAAAAAC‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:833336/88‑1 (MQ=255) gcTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt < 2:100965/90‑1 (MQ=255) ttttttCCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:872566/89‑1 (MQ=255) tttttCCCCCCCAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:391665/90‑1 (MQ=255) tttcCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:300595/90‑1 (MQ=255) tttcCCGCCCCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:811090/90‑1 (MQ=255) | CTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTG > NZ_CP009273/353502‑353677 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |