| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 51.8% | 33.3 / 77.3 | 56 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (21/6); new base A (0/29); total (21/35) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.20e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.95e-07 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGC > NZ_CP009273/353514‑353678 | aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGc‑aa‑caa > 1:956295/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑Caaa > 1:910955/1‑90 (MQ=255) tttCCGCAAACACCCGCGCTTTTACCCACCGCCATGGGAAAAAATGCCTTCGGGGCGGC‑TGTCTGCCAGCTTTTTTTCCGCCGC‑aa‑aaaa < 1:289747/90‑1 (MQ=18) gCCAACAACCGCGCATTTATCCAACGCCGTGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑ccgc > 1:501926/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑ccgc > 2:1354089/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑ccgc > 2:1223711/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑ccgc > 2:232060/1‑90 (MQ=255) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGtt > 1:1464047/1‑90 (MQ=255) cacccGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTTCGGGGCGGC‑TGTCTGCCAGTTTTTTTTCCGCCGC‑AA‑AAAAA‑CCGCCGTtc < 1:594092/87‑1 (MQ=21) cacccGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTTCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCGCCGC‑AA‑CAAAA‑CCGCCGTtc < 1:1233727/87‑1 (MQ=21) cacccGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGTTTTTTTCCCGCCGC‑AA‑AAAAA‑CCGCCGTtc < 1:1510432/87‑1 (MQ=21) cacccGCGCTTTTACCAACCCCCATGTGAAAAAATGCCTTCGGGGCGGT‑TGTCTGCCAGCTTTTTTCCCGCCGC‑AA‑CAAAA‑CCGCCGTtc < 1:193602/87‑1 (MQ=21) cacccGCGATTTTACCCAACGCCATGTAAAAAAATCCTTTCGCGGGGGC‑TGTCTGCAAGCTTTTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTtc < 1:1468368/87‑1 (MQ=255) cacccGCACATTTACCCAACGCCATGTGCAAAAATGCCTTCGGGGCGGC‑TGTCTGCCAGCTTTTTTTCCGCCGC‑AA‑AAAAA‑CCGCCGTtc < 1:598665/87‑1 (MQ=21) acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTtctc > 1:843073/1‑90 (MQ=255) ccGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTCCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCGCCGC‑AA‑AAAAA‑CCGCCGTtctct < 1:1465573/90‑1 (MQ=21) ccGCGCTTTTACCCACCCCCTTTTAAAAAAATGCCTTCGGGGGGGC‑TGTCTGCCATTTTTTTTCCCGCCGC‑AA‑CAAAA‑CCGCCGTtctct < 1:1001540/90‑1 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTcc > 2:1337510/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTcc > 2:1003752/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTcc > 2:1233727/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTcc > 2:1235932/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑CGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTcc > 2:1054335/1‑90 (MQ=255) cgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCa > 2:984464/1‑90 (MQ=255) cccACCGCCATGTAAAAAAATGCCTTCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCCCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:1230076/89‑1 (MQ=25) cccACCGCCATGTAAAAAAATCCCTTCGCGGCGGC‑TGTCTGCCAGCTTTTTTCCCGCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:914105/89‑1 (MQ=25) cccAACGCCATGTAAAAAAATCCCTTCGGGGCGGC‑TGTCTGCCAGTTTTTTTCCCCCCGA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:1302264/89‑1 (MQ=21) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCTGCTATTTTTCCGCCGC‑AA‑CAAAG‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1194558/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:131880/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:612668/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1437310/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:320044/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:844808/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCCC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1125720/1‑90 (MQ=255) aaaaaaTCCCTCCGGGGCGGC‑TGTCGGCCAGTTTTTTTCCCGCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:1409276/89‑1 (MQ=255) aaaaaTCCCTCCGGGGCGCT‑TTTCCCCCAGTTTTTTTCCCGCCGA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:550762/90‑1 (MQ=255) aaaaaT‑CCTTCGGGGGGGTTTGTCCGCCATTTTTTTTCCCGCCAA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:320195/90‑1 (MQ=255) aaaaaGGCCTTCGGGGCGGC‑TGTCTGCCAGCTTTTTTCCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:360930/90‑1 (MQ=255) aaaaaCCCCTCCGGGGGGGT‑TTTCGGCCAGTTTTTTTCCCGCCGA‑AA‑AAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:601343/90‑1 (MQ=255) tCGGGGCGGT‑TGTCTCCCAGTTTTTTTCCCGCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:809647/90‑1 (MQ=255) tCGCGGCGGC‑TTTTTGCCAGCTTTTTTCCCGCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:525790/90‑1 (MQ=255) tCGCGGCGGC‑TGTCTGCCAGTTTTTTTCCCGCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:593083/90‑1 (MQ=255) ggggggcggt‑TGTCTGCCAGTTTTTTTCCCGCCAC‑AA‑AAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:1334083/86‑1 (MQ=255) ccggggcggc‑TTTCTGCCATTTTTTTTCCCCCCGA‑AA‑AAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:843073/86‑1 (MQ=255) ccggggcggc‑TGTCTGCCAGTTTTTTTCCCCCCCA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:654878/86‑1 (MQ=255) ccggggcggc‑TGTCGCCCAGTTTTTTTCCCCCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:609623/86‑1 (MQ=255) gcggc‑TGTCTGCCAGCTTTTTTCCCGCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 1:61852/90‑1 (MQ=255) tGTCTGCAATTTTTTTTCCCGCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg < 1:1081992/90‑1 (MQ=255) aGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAGATTTAAAACCCCCCTGTTTTGTgggga > 1:460802/1‑87 (MQ=255) tttttcCCGCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:191097/89‑1 (MQ=255) tttttcCCGCCCA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:59675/89‑1 (MQ=255) tttttcCCCCCGC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:806070/89‑1 (MQ=255) tttttcCCCCCCC‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1337510/89‑1 (MQ=255) tttttCCCCCCCAAA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1199132/90‑1 (MQ=255) tttttCCCCCCA‑AA‑AAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:621784/90‑1 (MQ=255) ttttcCCACCGC‑AACCAACC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1363524/90‑1 (MQ=255) tttcCCGCCGA‑AA‑AAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:577362/90‑1 (MQ=255) ttcccgccgA‑AA‑AAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc < 1:716744/87‑1 (MQ=255) tccccgccgA‑AA‑AAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc < 1:1154688/87‑1 (MQ=255) | ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGC‑AA‑CAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGC > NZ_CP009273/353514‑353678 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |