| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 53.8% | 30.4 / 66.0 | 39 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (13/5); new base A (0/21); total (13/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.05e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.42e-06 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658973‑3659144 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc > 1:107871/1‑90 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:417117/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:929512/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 1:458280/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:196449/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:611276/1‑90 (MQ=255) aatGAAAGCGTTCCCTTTGACACAAAAAAAAAATTTTCAACACCCTTATCTACTCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCg < 1:223588/90‑1 (MQ=255) aatGAAAGCGTTCCCCTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCg < 1:175434/90‑1 (MQ=255) aatGAAAGCGTGTCCCTTGACACAAATAAAAAATTTTCAACACTTTTATCTACTCGATTTTGGCTTGCATCCGCAAAACCCAGGTCACCg < 2:516581/90‑1 (MQ=255) aaaaaaaGCGTTTCCTTTGACACAAATAAAAAATTTCCAACACCCTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCGGGTCACCg < 1:899658/86‑1 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:707549/1‑90 (MQ=255) aaGCGTGTCCCTTGACACAAATACAAAATTTTCAACACACTTATCTCCTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCAtt < 2:200663/90‑1 (MQ=255) tgtCCCTTGACACAAAAAAAAAATTTTCAACCCCCTTTTCTACTCGATTTTGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAAt < 1:282809/90‑1 (MQ=255) gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 1:921773/1‑90 (MQ=255) cctttGACACAAAAAAAAAATTTTCAACACCCTTATCTCCTCAATTTTGGTTTGCACCCAAAAAAACCAGGCCCCCGCCATTAAAATAGc < 1:605130/87‑1 (MQ=255) cTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGa < 2:218080/90‑1 (MQ=255) cTTGACACAAAAAAAAATTTTTCAACACACTTATCTCCTCAATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGa < 2:826650/90‑1 (MQ=255) ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat > 2:858561/1‑90 (MQ=255) tGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGata > 2:533548/1‑90 (MQ=255) tGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGata > 2:492328/1‑90 (MQ=255) cacGAAAAAAAAATTTTCACCCCCTTTATCTCCTAAATTTTGGTTTGCACCCAAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTc < 1:241026/90‑1 (MQ=255) aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCa > 2:805976/1‑90 (MQ=255) taaaCACCTTTTTCTACTCAATTTTGGTTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:276930/88‑1 (MQ=255) tCAACACATTTATCTACTAAATTTTGGTTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:582633/90‑1 (MQ=255) cccccTTATCTACTCAATTTTGGTTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:2057/86‑1 (MQ=255) cacccTTATCTACTAGATTTTGGTTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:435396/90‑1 (MQ=255) ccacTTATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:708758/89‑1 (MQ=255) ccacTTATCTACTCGATTTTGGCTTGCATCCGCAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:100358/89‑1 (MQ=255) cagtttATCTCTTCGATTTTGGCTTCCATCAAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:919851/86‑1 (MQ=255) acctttATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:213536/86‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:360916/1‑90 (MQ=255) tCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCt > 2:381476/1‑90 (MQ=255) cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtg > 1:919851/1‑89 (MQ=255) tggctggcACCCGAAAAAACCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:203286/90‑1 (MQ=255) tGGTTTGCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:227470/90‑1 (MQ=255) tGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:492846/90‑1 (MQ=255) tGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:68701/90‑1 (MQ=255) tGGCTTCCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:184690/90‑1 (MQ=255) gggCTTACATCCCAAAAAACCGGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:490875/89‑1 (MQ=255) gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 1:105148/1‑90 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658973‑3659144 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |