| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,906,007 | 0 | T | G | 55.6% | 17.2 / 27.6 | 27 | H276P (CAC→CCC) | htpX | protease HtpX |
| Reads supporting (aligned to +/- strand): ref base T (3/9); new base G (15/0); total (18/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.69e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.36e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGT > NZ_CP009273/1905919‑1906095 | gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg < 1:1060383/90‑1 (MQ=255)gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg < 1:1188766/90‑1 (MQ=255)gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg < 1:846757/90‑1 (MQ=255) cTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGaacaa < 1:1039552/90‑1 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg < 2:159895/66‑1 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg > 1:159895/1‑66 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGTATTAAAAAATTACTGAGCgg > 2:1549026/1‑89 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGATGAAAAACTCACTTAGCgg > 1:525533/1‑89 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCGTTAACAAAACACTTAGCgg > 2:1069668/1‑89 (MQ=255) tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAATCAATCAGCGa > 2:1422352/1‑90 (MQ=255) cATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCg > 1:209673/1‑90 (MQ=255) cATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGATTAAAAACACACCGAGCGGttttt > 2:652819/1‑88 (MQ=255) tatTGCTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCGGGAAAAAATCACTGGGCGAttttggg > 1:1355084/1‑86 (MQ=255) cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTTcc > 1:1344610/1‑90 (MQ=255) tCAGGTATTCACCCGTACGCAGATCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGATTAAAAACTCCCTGAGCGATTTTGACTTACCGt > 1:1590746/1‑90 (MQ=255) cAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGtt < 2:209673/90‑1 (MQ=255) cAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGGACAAAACACCGAGCGATTTTTACTTACCGtt > 2:805786/1‑90 (MQ=255) aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTTAGCGATTTTGACTTACCGTTa > 1:1243780/1‑90 (MQ=255) gTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAAt < 1:1069668/90‑1 (MQ=255) aTTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAACCCCCGAGCGATTTTGTCTTACCGTTGATgg > 2:687326/1‑89 (MQ=255) tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCag > 1:1559342/1‑90 (MQ=255) tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCGTTAATGCag > 1:1059930/1‑90 (MQ=255) tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAACAAAACACCGAGCGGTTTTGACTTACCGTTAATGCag > 2:1361941/1‑90 (MQ=255) cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga < 2:1107812/90‑1 (MQ=255) cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga < 1:1217767/90‑1 (MQ=255) cGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGc < 2:1559342/90‑1 (MQ=255) cGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGc < 1:696847/90‑1 (MQ=255) aCGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTGACTTTCCGTTTATGCAGAGAGCcat > 2:867870/1‑90 (MQ=255) gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAACCACTGAGCGATTTCGACTTACCCTTGATGCAGAGAGCCATCATGc > 2:352884/1‑90 (MQ=255) ttCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGt < 1:1178070/90‑1 (MQ=255) tCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAATCACCGAGCGGGTTTGGCTTACCCTTAATGGAGAGAGGCATCATACTGGtt > 2:530182/1‑90 (MQ=255) agaTCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGc < 1:1345050/88‑1 (MQ=255) ggggggggCATGAAAAACTCACTGAGCGGTTTCGCCTTACCGTTAATGCAGAGAGCCAACATGGTGGGTGCTTCTTTCGGTTCATAGcct > 2:1345050/1‑88 (MQ=255) gtgggtCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGt < 2:45330/90‑1 (MQ=255) | GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGT > NZ_CP009273/1905919‑1906095 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |