| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 52.6% | 12.3 / 30.8 | 19 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (7/2); new base A (0/10); total (7/12) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.14e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-04 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAA > NZ_CP009273/3658977‑3659150 | aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 2:167600/1‑90 (MQ=255) gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑cc < 1:332967/90‑1 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCAtt > 2:269403/1‑90 (MQ=255) gCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTaa > 1:233743/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTaaaa > 2:82200/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTAAAATa > 2:276358/1‑90 (MQ=255) cccTTGACACAAATACAAAATTTT‑CAA‑CACCTTTATCTACTCAATTTTGGCTTCCACCCGAAAAAC‑CCAGGCCCCCGCCATTAAAATAGc < 2:174042/90‑1 (MQ=255) ccTTTACCCCAAAACAAAAATTT‑CAACCCCATTTATCTACAAAATTTTGGCTTCCACCCCAAAAAA‑CAAGGCCACCGCCATTAAAATAGc < 2:233743/90‑1 (MQ=255) cacaAAAACAAATTTTC‑CAC‑CCCACTTTTCTACAC‑AATTTTGCTTTCCACCACAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTc < 2:202155/90‑1 (MQ=255) tACAAATTTTT‑CAA‑CCCACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:10481/90‑1 (MQ=255) taaaaaTTTTCCAA‑CACCCTTATCTACCCAATTTTGGCTTCCCCCCAAAAAAA‑CCGGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:49101/88‑1 (MQ=255) ttta‑CAA‑CACATTTATCTCCTCAATTTGGGCTTCCACCCAAAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg < 2:115361/90‑1 (MQ=255) t‑CAA‑CCCCCTTATCTACTCAAATTTGGTTGCCACCCAAAAAAA‑CCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:189533/90‑1 (MQ=255) t‑CAA‑CACATTTATCTCCTCGATTTTGGTTTGCACCCGAAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:30964/90‑1 (MQ=255) ccAA‑CCCACTTATCTCCTCAATTTTGGTTTGCACCCGAAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:291366/89‑1 (MQ=255) acccTTATCTCCTCTATTTTGGCTTCCACCCGAAAAAA‑CCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:276358/87‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:63326/1‑90 (MQ=255) tGGCTTCCACCCAAAAAAC‑CCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:82200/90‑1 (MQ=255) gCAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAcct > 1:36616/1‑88 (MQ=255) | ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAA‑CCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAA > NZ_CP009273/3658977‑3659150 |
| 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: ‑ |