| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 51.7% | 29.2 / 56.8 | 29 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (10/4); new base A (0/15); total (10/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.00e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.77e-06 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACA > NZ_CP009273/3658975‑3659149 | gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:640492/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:695300/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:590256/90‑1 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:496022/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:214443/1‑90 (MQ=255) agaAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAgg > 2:71393/1‑90 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 1:136599/1‑90 (MQ=255) cGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaa > 1:339694/1‑90 (MQ=255) tgccccTTAACACAAATAAAAAATTTTCAACACCTTTATCTCCCCAATTTTGTCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAAt < 2:209777/87‑1 (MQ=255) gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 1:628519/1‑90 (MQ=255) cccTTGACACAAATAAAAAATTTTCAACACACTTATCTCCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGc < 1:92135/90‑1 (MQ=255) cTTAACACAAAAAAAAAATTTCCACCCCCCTTATTTCCTCAATTTTGGCTTCCACCCGAAAAACCCAGGCCCCCGCCATTAAAATAGCGa < 2:628519/90‑1 (MQ=255) gACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGatat > 2:405231/1‑90 (MQ=255) cacaAATAAAAAATTTTCAACACCCTTATCTCCTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:78105/90‑1 (MQ=255) taaaaatTTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:214443/87‑1 (MQ=255) aaaaaatTTTTCAACCCCTTTATCTCCTCGATTTTGGTTTGCACCCGAAAAACCCGGGCCACCGCCATTAAAATAGCGATATTCACCAtt < 1:496022/87‑1 (MQ=255) ttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt > 1:467837/1‑90 (MQ=255) taaaCACTTTTATCTCCTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:691443/88‑1 (MQ=255) taaaCACATTTATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:452299/88‑1 (MQ=255) tCAACCCATTTATCTACTCAAATTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:659067/90‑1 (MQ=255) tCAACACTCTTATCTACTCAATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:136599/90‑1 (MQ=255) tCAACACATTTATCTCCTCGATTTTGGCTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:71393/90‑1 (MQ=255) tCAACACATTTATCTACTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:666289/90‑1 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:80039/1‑90 (MQ=255) tGGTTTCCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:169856/90‑1 (MQ=255) tGGCTTGCACCCGAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:209847/90‑1 (MQ=255) tGGCTTGCACCCAAAAAACCAAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:705090/90‑1 (MQ=255) tGGCTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:80039/90‑1 (MQ=255) cGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACa > 2:424258/1‑90 (MQ=255) | GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACA > NZ_CP009273/3658975‑3659149 |
| 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: ‑ |