| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 54.5% | 23.4 / 40.7 | 22 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (8/2); new base A (0/12); total (8/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.41e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.83e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 | gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:462246/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:345392/90‑1 (MQ=255) aatAAAGGCGTGCCCCTTGACACAAAAAAAAATTTTT‑CAACCCCTTTTTCTACTCGATTTTGGCTTCCACCCGAAAAAACCAGGTCACCg < 2:106054/90‑1 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 1:84784/1‑90 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:122787/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 1:259643/1‑90 (MQ=255) aaTACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCa < 1:479643/90‑1 (MQ=255) aaaaaaaaTTTCCCAACACATTTATCCCCTAAATTTTGGTTTGCACCCAAAAAAACCGGGCCCCCGCCATTAAAATAGCGATATTCACCa < 2:397465/86‑1 (MQ=255) aaTTTT‑CAACACATTTATCTCCTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:141529/90‑1 (MQ=255) t‑CACCACATTTATCTCCTCAAATTTGGCTTGCACCCCAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:108543/90‑1 (MQ=255) t‑CAACACACTTATCTACTCAATTTTGGCTCCCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:305716/90‑1 (MQ=255) taaaCACATTTATCTCCTCAATTTTGGTTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:104835/88‑1 (MQ=255) ccacTTATCTACTCGATTTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:136394/89‑1 (MQ=255) tACTCAATTTTGGCTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg < 2:174729/90‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg > 2:71559/1‑71 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:384738/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg < 1:71559/71‑1 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:318581/1‑90 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:264264/1‑90 (MQ=255) ttGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa > 1:250281/1‑90 (MQ=255) tGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:177807/90‑1 (MQ=255) tGGCTTGCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:459871/90‑1 (MQ=255) | GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |