Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NZ_CP009273 | 2,147,725 | 0 | A | C | 53.3% | 19.0 / 20.5 | 15 | T77P (ACC→CCC) | mdtA | multidrug efflux RND transporter subunit MdtA |
Reads supporting (aligned to +/- strand): ref base A (6/1); new base C (0/8); total (6/9) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 1.40e-03 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.72e-04 | |||||||||||
Rejected as consensus: Frequency below/above cutoff threshold. |
CGTTCCGGCCCATTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTACATTTCCAGGA > NZ_CP009273/2147659‑2147810 | cGTTCCGGCCCATTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTAccgcc > 1:293477/1‑90 (MQ=255) ttCCGGCCCATTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACcgccgc > 2:179552/1‑90 (MQ=255) cGGCCCATTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTaa > 1:779179/1‑90 (MQ=255) aTTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGt > 1:276926/1‑90 (MQ=255) cccccGGTTCGGGGGCGCCCCCCCCGTAGAACAGGCAGTCCCGCTTTCCCTCCCCGGGCTTGGCCCCATTACCGCCGCTAATACCGTTAc < 2:105793/89‑1 (MQ=255) cgACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTgg > 2:294862/1‑90 (MQ=255) ccccgccgTAGAACAGGCATTCCCGCGTTCCCCCCCCGGGCTTGGCCCCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGa < 2:293477/88‑1 (MQ=255) ccgccgTAGAACAGGCAGTTCCGCGTTCCCTCCCCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACg < 1:180057/90‑1 (MQ=255) gccgTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGc < 1:294862/90‑1 (MQ=255) cccgTAAAACGGGCATTTCCGCTTTCCCTCCCCGGGCTGGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGc < 1:792277/89‑1 (MQ=255) ggCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGc > 2:280215/1‑90 (MQ=255) ggCAGTCCCGCTTTCCCCCCCCGGGCTGGGCCCCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGc < 1:478238/90‑1 (MQ=255) gTTCCGCGTTCCCTCCCCGGGCTTGGCCCCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTa < 1:209426/90‑1 (MQ=255) tcccGCGTTCCCCCCCGGGGCTGGGCCCCATTCCCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTAc < 2:108601/88‑1 (MQ=255) ccTCCCCGGGCTGGGCCCCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTACATTTCCAGGa < 1:179552/90‑1 (MQ=255) | CGTTCCGGCCCATTAGCCCCGGTTCAGGCG‑GCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTACATTTCCAGGA > NZ_CP009273/2147659‑2147810 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |