| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 56.7% | 18.3 / 51.1 | 30 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (11/2); new base A (0/17); total (11/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.43e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.53e-06 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658973‑3659144 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGc > 2:610195/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:178606/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:632749/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:867586/1‑90 (MQ=255) cgtCCATTG‑ACCCGAATAAAAAATTTT‑CAACACACTTATCTACTCTACTTTGGTTTGTAACCGAAAAACCTAGTTCACCGCCATTAAAAt < 2:418609/89‑1 (MQ=255) gtCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:391331/1‑90 (MQ=255) cccTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGc > 2:500088/1‑90 (MQ=255) ccTTGAACACAAATAAAAAATTTT‑CAACACACTTATCTACCCAATTTTGGCTGCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc < 2:420347/90‑1 (MQ=255) cTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGACACCGCCATTAAAATAGCGa < 2:233842/90‑1 (MQ=255) cTTG‑ACACAAATAAAAATTTTT‑AAACCCCTTTATTTCCTCAATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGa < 2:431291/90‑1 (MQ=255) cTTG‑ACAAAAATAAAAAATTTA‑CAACCCCCTTATCCACTAAATTTTGGCTTCCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGa < 1:669404/90‑1 (MQ=255) ttG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat > 2:844505/1‑90 (MQ=255) cacaAATAAAAATTTTT‑CAACCCCCTTTTCTCCTCAATTTTGGCTTCCACCCCAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:537981/90‑1 (MQ=255) cacaAATAAAAATTTTT‑CAACCCACTTATCTCCTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 2:322371/90‑1 (MQ=255) aaaaaaTAAAAATTTTT‑CAACCCTCTTTTTTCCTAAATTTTGGTTTCCATCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTc < 1:610195/86‑1 (MQ=255) aaaaaaaaTTTTCCAACCCCTTTTTCTCCTCAATTTTGGTTTCCACCCCAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTCACCa < 1:500088/86‑1 (MQ=255) taaaaaaTTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:178606/87‑1 (MQ=255) attttt‑CAACACACTTATCTACTAAATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:844505/88‑1 (MQ=255) aaTTTC‑CACCACCCTTATCTACTAAATTTTGGTTTCCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:391331/90‑1 (MQ=255) tt‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 1:578374/1‑41 (MQ=255) tt‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:578374/41‑1 (MQ=255) ccatttATCTACTAAAATTTGGCTTCCACCCGAAAAAACAAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:550802/86‑1 (MQ=255) acatTTATCTACTAGATTTTGGCTTGCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:143376/90‑1 (MQ=255) cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata > 1:347440/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:795496/1‑90 (MQ=255) cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt > 1:337809/1‑90 (MQ=255) aaaTTTGGCTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTg < 1:200667/89‑1 (MQ=255) tGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:119773/90‑1 (MQ=255) tGGCTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:632749/90‑1 (MQ=255) ggccTTGCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:754561/87‑1 (MQ=255) gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 1:693836/1‑90 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > 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: ‑ |