| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 52.9% | 52.0 / 99.9 | 51 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (19/5); new base A (0/27); total (19/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 8.77e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.32e-11 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAT > NZ_CP009273/3658975‑3659151 | gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:1179546/90‑1 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaa > 1:201624/1‑90 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaa > 1:787619/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:424408/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc > 2:171454/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc > 1:563918/1‑90 (MQ=255) gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAGCACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc < 2:304902/90‑1 (MQ=255) ggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCa < 1:1240823/90‑1 (MQ=255) aatGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCg < 2:65245/90‑1 (MQ=255) aatGAAAGCGTCCCCCTTGACAAAAATAAAAAATTTT‑CAACACACTTATCTCCTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCg < 2:1109574/90‑1 (MQ=255) aatAAAAGCGTTCCCCTTACCACAAATAAAAAATTTT‑CACCACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCg < 1:171454/90‑1 (MQ=255) aatAAAAGCGTGTCCTTTGACACGAATAAAAAATTTT‑CAACACACTTATCTCCTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCg < 2:563918/90‑1 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 2:253327/1‑90 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 2:684312/1‑90 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 1:570066/1‑90 (MQ=255) aaGCGTGTCCCTTGACACAAATAAAAAATTTT‑CAACACACTTATCTCCTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCAtt < 2:31628/90‑1 (MQ=255) gCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaa > 1:1146709/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:555653/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 1:213707/1‑90 (MQ=255) cccTTGACACAAATACAAAATTTT‑CAACACCCTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc < 2:165232/90‑1 (MQ=255) cccTTGACACAAATAAAAAATTTT‑CAACACATTTTTCTACTAAATTTTGGCTTGCACCCGAAAAACCCAGGCCCCCGCCATTAAAATAGc < 1:27639/90‑1 (MQ=255) cacaAATACAAAATTTT‑CAACCCATTTATCTCCTCAATTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 2:1957/90‑1 (MQ=255) cacaAATAAAAATTTTT‑AAACCCCCTTATCTACTCGATTTTGGCTTGCATCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTc < 2:1255555/90‑1 (MQ=255) caaaTAAAAATTTTC‑CAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAc < 2:572008/88‑1 (MQ=255) gAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc > 2:447512/1‑90 (MQ=255) gAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc > 1:766597/1‑90 (MQ=255) gAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc > 1:1362035/1‑90 (MQ=255) aTACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAt > 2:942538/1‑90 (MQ=255) aaaaaaaTTTA‑CAACCCCTTTATCTCCCCAATTTTGGTTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:1171643/87‑1 (MQ=255) aaaaaaTTTTCCAACCCCCTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:555653/88‑1 (MQ=255) aaatTTTT‑CAACACTCTTATCTCCTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAAc < 2:1083385/90‑1 (MQ=255) aaTTTC‑CAACCCACTTATCTCCTAAAATTTGGCTTCCACCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:389065/90‑1 (MQ=255) tttt‑AAACCCATTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg < 2:1189981/90‑1 (MQ=255) ttcaaaCACATTTTTCTCCTCAATTTTGGCTTCCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg < 2:650327/86‑1 (MQ=255) aaaCCCATTTATCTCCTCAATTTTGGCTTCCACCCGAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga < 2:283697/89‑1 (MQ=255) cctttATCTCCTGGATTTTGGCTTGCATCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata < 2:766597/87‑1 (MQ=255) tctcCTCAATTTTGGCTCGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTa < 2:170575/90‑1 (MQ=255) cTCGATTTTGGCTTGCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc < 1:1357544/90‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:100132/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:498729/1‑90 (MQ=255) tGGCTTGCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:570066/90‑1 (MQ=255) tGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:297087/90‑1 (MQ=255) tGGCTTCCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:227662/90‑1 (MQ=255) tGGCTTCCACCCCAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:684312/90‑1 (MQ=255) tGGCTTCCACCCAAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:424408/90‑1 (MQ=255) tGGCTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:1362035/90‑1 (MQ=255) ggCTTGCATCCGCAAAAACCAGGTCACCGACATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:345774/89‑1 (MQ=255) ggCTTGCATCCGCAAAAACCAGGTCACCGACATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc > 1:345774/1‑89 (MQ=255) gtttGCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGc < 1:818085/88‑1 (MQ=255) ccGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc < 2:213707/90‑1 (MQ=255) cGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACa > 1:275267/1‑90 (MQ=255) cAAAAACCAGGTCACCGACATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt < 2:1197088/90‑1 (MQ=255) | GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAT > NZ_CP009273/3658975‑3659151 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |