| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 54.7% | 24.5 / 67.7 | 53 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (19/5); new base A (1/28); total (20/33) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.14e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-06 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAT > NZ_CP009273/353515‑353688 | tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa > 2:882436/1‑90 (MQ=255)tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa > 2:1496499/1‑90 (MQ=255)tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa > 2:723030/1‑90 (MQ=255) cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg > 1:2260540/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc > 1:1610022/1‑90 (MQ=255) ccaaacaccCCCGCTTTTACCCAACGCCATGTGCAAAAAGGCTTC‑CGGGGGGGTTGTCTCCCAGTTTTTTTCCCGCCGCAACAAAAccgc < 1:1337231/87‑1 (MQ=255) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt > 2:1092237/1‑90 (MQ=255) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt > 2:1176897/1‑90 (MQ=255) cacccGCGCTTTTACCCACCGCCATGTGAAAAAATGCTTT‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTtc < 1:645066/87‑1 (MQ=21) cacccGCGCTTTTACCCAACCCCATGTGAAAAAATGCCTT‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTtc < 1:2059928/87‑1 (MQ=21) cacccGCGCTTTTACCCAACCCCATGTAAAAAAATCCTTC‑CGGGGGGGCTGTCTCCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTtc < 1:1908182/87‑1 (MQ=255) cacccGCGCATTTACCCAACCCCATGTGAAAAAATGCCTT‑CGCGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTtc < 1:2189284/87‑1 (MQ=21) acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc > 1:2253624/1‑90 (MQ=255) ccGCCCTTTTACCCACCCCCATGTAAAAAAATGCCTC‑CGCGGCGCCTGTCTGCCAGCTTTTTTCCCGCCCCAACAAAACCGCCGTtctct < 1:1442782/90‑1 (MQ=255) gcgcTTTTACCCACCGCAATGTGAAAAAATGCCTT‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTcc < 1:848371/90‑1 (MQ=21) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctct > 1:1149947/1‑89 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc > 2:773916/1‑90 (MQ=255) ccgcTTTTACCCACCCCCATGTGAAAAATTGCCTT‑CGCGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTcc < 1:723030/89‑1 (MQ=21) ttttACCCACCCCCAGGTAAAAAAATCCCTC‑GGGGGGGGTTTTCTCCCGGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCagta < 2:1804935/89‑1 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc > 2:311099/1‑80 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc < 1:311099/80‑1 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag > 1:440073/1‑90 (MQ=255) aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg > 2:1258595/1‑90 (MQ=255) aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg > 2:1348705/1‑90 (MQ=255) cccccATGGGAAAAAATGCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCgggg < 1:2083540/87‑1 (MQ=25) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:334574/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1804935/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1763960/1‑90 (MQ=255) cATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggtag > 2:2054061/1‑86 (MQ=255) aTGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCgaga > 1:1008085/1‑90 (MQ=255) aTGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGagg > 2:992495/1‑89 (MQ=255) aaaaaaTGCCTT‑CGCGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:306801/89‑1 (MQ=38) aaaaaTCCCTC‑GGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:847532/90‑1 (MQ=255) aaaaaTCCCTC‑CGGGGGGGTTGTCTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:440073/90‑1 (MQ=255) aaaaaCCCCTC‑CGGGGCGGTTTCCCGCCAGTTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:1688543/90‑1 (MQ=255) aaaaTGCCTTCCGCGGGGGTTTTCGGCCAGTTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:1693681/90‑1 (MQ=255) ctccgcgGGGGTTGGCTCCCAGTTTTTTTCCCCCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg < 1:1116571/87‑1 (MQ=255) t‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:980541/90‑1 (MQ=255) ccggggcggcTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:313114/86‑1 (MQ=255) cggcggCTGTCGGCCAGCTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt < 1:374652/90‑1 (MQ=255) gcggcTGTCTCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 1:1464570/90‑1 (MQ=255) gttGTCTGCCACTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt < 1:1687085/88‑1 (MQ=255) tttttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:681215/87‑1 (MQ=255) tttttcCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:348443/89‑1 (MQ=255) tttttcCCCCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:703791/89‑1 (MQ=255) tttttcCCCCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1866716/89‑1 (MQ=255) tttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:1270612/90‑1 (MQ=255) ttccccgccaCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:1381513/86‑1 (MQ=255) tcccgccgAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 1:340363/88‑1 (MQ=255) tcccgcccCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 1:773916/88‑1 (MQ=255) tcccgccaAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 2:878758/88‑1 (MQ=255) ccccccgaAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg < 1:112068/86‑1 (MQ=255) gccgaAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:1062636/90‑1 (MQ=255) cccacaaaaaACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:1572382/86‑1 (MQ=255) aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt < 1:2071070/90‑1 (MQ=255) | TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAT > NZ_CP009273/353515‑353688 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |