| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 55.2% | 12.3 / 30.4 | 29 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (9/4); new base A (0/16); total (9/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.14e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.37e-03 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTA > NZ_CP009273/353523‑353683 | aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt > 1:1124077/1‑90 (MQ=255) cacccGCGCTTTTATCCAACGCCATGTGAAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTTCCGCCGCAAAAAAACCGCCGTtc < 2:1077356/87‑1 (MQ=21) cacccGCGCTTTTACCCACCCCCTTGTG‑AAAAATGCCCTT‑CGCGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTtc < 2:715100/87‑1 (MQ=255) ccGCGCTTTTACCCAACCCCATGTGAAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTtctct < 2:1043565/90‑1 (MQ=25) ccGCGATTTTATCCACCCCCTTGTGAAAAAATG‑CCTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTtctct < 2:1124077/90‑1 (MQ=25) gcgcATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc > 1:557449/1‑90 (MQ=255) gcgcATTTACCCACCCCAATGTGAAAAAATG‑CCTT‑CGGGGCGCCTGTCTCCCAGCTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTcc < 2:165777/90‑1 (MQ=255) cgcATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCa > 1:159314/1‑90 (MQ=255) cccACCGCAATGTG‑AAAAAAG‑CCTTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc < 2:1131367/89‑1 (MQ=255) ccaaaCGCCTTGTCAAAAATTT‑CCTT‑CGGGGGGCCTCCCCGCCAGTTTTTTTTCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGc < 2:667318/87‑1 (MQ=255) aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:285280/1‑90 (MQ=255) aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1137999/1‑90 (MQ=255) aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1119834/1‑90 (MQ=255) aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:590008/1‑90 (MQ=255) aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg > 1:514276/1‑90 (MQ=255) aaaagTC‑CCTC‑CGGGGCGGCTTTCTCCCGTCTTTTTTGCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:788039/90‑1 (MQ=255) aaaaaTC‑CCTC‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:735710/90‑1 (MQ=255) tcccTC‑CGGGGCGGCTGTCTCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt < 2:882600/88‑1 (MQ=255) t‑CGGGGGGGCTGTCTCCCAGTTTTTTTCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:841433/90‑1 (MQ=255) t‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:1331504/90‑1 (MQ=255) ccggggcggtGGTCTGCCAGCTTTTTTTCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:1099553/86‑1 (MQ=255) ccgcgGGGGCTTTCTCCCGTTTTTTTTCCCCCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:1154375/89‑1 (MQ=255) gcggcTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 2:1290062/90‑1 (MQ=255) gggcTGTCTGCGGGTTTTTTTCCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt < 2:1209035/89‑1 (MQ=255) tttttcCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:665503/89‑1 (MQ=255) tttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:997557/89‑1 (MQ=255) tttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:159314/89‑1 (MQ=255) tttcCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:93893/90‑1 (MQ=255) gccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAAAAAAAACTTTAAACCCCCCATGTTTTTTTGGAAAAGCTGCTgggg > 1:444079/1‑88 (MQ=255) | AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTA > NZ_CP009273/353523‑353683 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |