| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 48.7% | 38.7 / 26.4 | 39 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (17/3); new base A (0/19); total (17/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.57e-08 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658977‑3659144 | aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 2:1236003/1‑90 (MQ=255)aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 1:1280071/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:649027/1‑90 (MQ=255) gaAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGt > 2:682764/1‑90 (MQ=255) aatAAAAGCGTGCCCCTTGACACAAATAAAAAATTTT‑CAACACACTTATCTACTCGATTTTGGCTTCCACCCGCAAAACCCAGGTCACCg < 1:1248765/90‑1 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:85271/1‑90 (MQ=255) aaGCGTGTCCCTTGACACAAATAAAAATTTTT‑CAACACTTTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCAtt < 1:738676/90‑1 (MQ=255) cGTGCCCCTTGACACAAATAAAAAATTTT‑CAACCCACTTATCTCCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaa < 1:1425/90‑1 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:1248765/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:1321473/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:183163/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:608178/1‑90 (MQ=255) cccTTGACACAAATAAAAATTTTT‑CAACACACTTATCTCCTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGc < 1:1204198/90‑1 (MQ=255) cccTTGACACAAATAAAAAATTTC‑CAACACACTTATCTACTCAATTTTGGCTTCCACCCAAAAAAACCAGGCCACCGCCATTAAAATAGc < 2:1280071/90‑1 (MQ=255) cTTGACACAAATAAAAAATTTT‑CAACCCACTTATCTCCTCGATTTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGa < 1:57017/90‑1 (MQ=255) cTTGACACAAATAAAAAATTTT‑AAACACACTTATCTCCTCGATTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGa < 1:1236003/90‑1 (MQ=255) cTTGACAAAAAAAAAAATTTTT‑CAACACCCTTATCTACTCAAATTTGGTTTGCACCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGa < 1:1321473/90‑1 (MQ=255) cTTCACACAAAAAAAAAATTTC‑CAACCCATTTATCTACTCGATTTTGGTTTGCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGa < 2:664199/90‑1 (MQ=255) cacaAATAAAAATTTTT‑CAACACTCTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 2:481272/90‑1 (MQ=255) cacaAATAAAAAATTTT‑CAACACCCTTATCTACTCGATTTTGGCTTGCATCCGAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTc < 1:201849/90‑1 (MQ=255) cacaAATAAAAAAATTT‑AAACCCACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 1:525569/90‑1 (MQ=255) caaaTAAAAAATTTT‑CAACACCCTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAc < 1:85271/88‑1 (MQ=255) gAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc > 2:933790/1‑90 (MQ=255) aaaaaaaTTTC‑CAACACATTTACCTACACGAATTTGGCTTCCCCCCAAAAAACCCGGCCCCCCGCCATTAAAATAGCGATATTCACCAtt < 2:1276995/87‑1 (MQ=255) aaaaaaTTTTCCAACCCTTTTTTCTTCTCAATTTTGGCTTCCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:1305219/88‑1 (MQ=255) aCAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTa > 2:179293/1‑90 (MQ=255) t‑CAACACATTTATCTCCTCGATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:1333076/90‑1 (MQ=255) taaccactcTTATCTACTCAATTTTGGTTTGCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:1188120/86‑1 (MQ=255) aaCCCATTTATCTACTCGATTTTGGTTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag < 1:1319133/90‑1 (MQ=255) aaCACTCTTATCTCCTCGAATTTGGCTTGCATCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag < 1:1048407/90‑1 (MQ=255) aaCAAATTTATCCCCTCGATTTTGGCTTGCAACCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag < 1:183163/90‑1 (MQ=255) cTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTAt > 2:1262819/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:468319/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:590459/1‑90 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg > 2:242565/1‑70 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:208548/1‑90 (MQ=255) aaTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:242565/70‑1 (MQ=255) tGGCTTCCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:768484/90‑1 (MQ=255) gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 2:563351/1‑90 (MQ=255) | ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658977‑3659144 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |