| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 55.6% | 14.7 / 40.3 | 27 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (9/3); new base A (0/15); total (9/18) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.69e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 | gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:402655/90‑1 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaa > 2:187178/1‑90 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 1:276349/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:661893/1‑90 (MQ=255) cGTGTCCCTTGACACGAATAAAAAATTTTC‑AACACCTTTATCTCCTCGATTTTGGCTTGCCTCCGAAAAAACCAGGTCACCGCCATTaaa < 1:661893/90‑1 (MQ=255) gtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:227652/1‑90 (MQ=255) cccTTGACACGAATACAAAATTTTC‑AACACATTTATCTCCTCGATTTTGGCTTGCATCCGCAAAACCCAGGTCACCGCCATTAAAATAGc < 1:56730/90‑1 (MQ=255) cccTTAACACAAAAAAAAATTTTTC‑AACACACTTATCTCCTCGAATTTGGCTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGc < 1:778866/90‑1 (MQ=255) cacaAATAAAAATTTTCC‑AACCCATTTATCTACTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:164786/90‑1 (MQ=255) gAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc > 1:723163/1‑90 (MQ=255) aaaaaaaaTTTTCAAACACATTTTTTTCCTCAATTTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCa < 1:689523/86‑1 (MQ=255) taaaaatTTTTC‑AACACACTTATCTCCTCGATTTTGGCTTGCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCAtt < 1:665172/87‑1 (MQ=255) aaaTTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc > 1:495220/1‑90 (MQ=255) aaTTTTC‑AACACCCTTATCTACTCAAATTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:101720/90‑1 (MQ=255) aaTTTTA‑AACACTCTTATCTCCTCAATTTTGGCTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 2:224470/90‑1 (MQ=255) ttttC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg > 1:530182/1‑90 (MQ=255) tC‑AACCCATTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:603531/90‑1 (MQ=255) tC‑AACCCACTTATCTCCTCGAATTTGCCTTCCATCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:530182/90‑1 (MQ=255) tC‑AACACACTTATCTCCTCAAATTTGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:187178/90‑1 (MQ=255) cc‑AACCCACTTATCTCCCCAATTTTGGCTTCCCCCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:394577/89‑1 (MQ=255) cc‑AACACCTTTATCTACTAAATTTTGGTTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:801044/89‑1 (MQ=255) cagacacatTTATCTACTAAATTTTGGTTTGCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:216424/87‑1 (MQ=255) cacccTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:178674/90‑1 (MQ=255) tCTACTCAATTTGGGCTTCCCCCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTa < 1:582765/90‑1 (MQ=255) cTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttctg > 1:216424/1‑87 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:246117/1‑90 (MQ=255) tgccTTGCCCCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:411260/87‑1 (MQ=255) | GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |