| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 981,654 | Δ2 bp | 100% | coding (784‑785/1089 nt) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 981,654 | 0 | A | . | 95.3% | 169.6 / 2.8 | 43 | coding (785/1089 nt) | ompF | outer membrane porin 1a (Ia;b;F) |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base . (22/19); total (23/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01 | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 981,655 | 0 | T | . | 93.0% | 159.7 / 6.0 | 43 | coding (784/1089 nt) | ompF | outer membrane porin 1a (Ia;b;F) |
| Reads supporting (aligned to +/- strand): ref base T (2/1); new base . (21/19); total (23/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01 | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
TAGTCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTGATCGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCACCAACGATACCAAAGCCTTCGTATTCGTAGCTGATAGAACCGCCAACACCGTCGCCGTTAGAACGGCGTGCAGTGTCACGCTCG > CP009273/981435‑981890 || tAGTCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTTGCGCACACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGAGGAACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCTTTTTGTTGGCGAAGCCGCTGTTGTTTGTAAATATATTAGTG‑‑CGGCGAAGCGTTACTGGTTTCACTGTAGTTCGCTGCCAGGTAAATGCTGTTCTcgt > 1:268364/1‑275 (MQ=255) tAGGTGGACATGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCGTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGAAACTAACAGAACGTCTTGCGTTTTGTTGGCTAAGCCGCTGGTGTTTGTAAAGTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCa < 1:150750/275‑1 (MQ=255) gACATGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTCACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGc > 1:747723/1‑240 (MQ=255) tGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAgg < 2:747717/240‑1 (MQ=255) tGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTGTTGTTGGCGAAGCCGCTGGCGTTTGTAAATTTATTAGTG‑‑CGGCGTAGc > 1:15161/1‑187 (MQ=255) cgcCCACTTCCAAGTAGTTCGCCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTTGTGTAAGCGATGGACGGACGCAGACCGAACTCGAACTGGTCTTGCGCAACTAACAGAACGTCTTGCGTTTTGATGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTACACCGTAGTTCGCTGCCCGGTAGATGTTGTTCGCGTCGTACTTCAGACAAGTAGCCCACTGTTCAGCTTTTTTAcc > 1:790754/1‑272 (MQ=255) ggccACTTTAAAGTAGTTCGCCAGATCAACATCACAGATACCTTCTACGTCTTTCGCTTTGGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAAGCGAACTGGTATTGCGCAACTAACAGAACGTCTGGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTg < 2:790748/273‑1 (MQ=255) cccACGTCAAAGTAGTTCACCATATCAACATCTACGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGAGGCAGACCGAAAGCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTa < 2:15161/187‑1 (MQ=255) ttCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTcgc > 1:608543/1‑213 (MQ=255) cACCAGAACAACATCAACGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGACGGCCGGACGCAGACAGAAATCGAACTGGTATTGCGCAACTACCAGAACGTCTTGCGTTTTGTTGGCGAAGACGCTGGTGTTTGTAAATGTATTAGTG‑‑CGGCGTAGCGTTACAGGTTTCACCGTTGTTCGCTGCCAGGTAGATGTAGTTCGCGCAGTACTTCTGACAAGTAGACCACTGCGCCGCTGTTTTCCCGTCGCAAAGCGCTTGGGctccg > 2:208265/1‑272 (MQ=255) ccAGATCAACATCACCTATACCTTCTTCGTCTATCGCTTACGATTTGGTGTAAGCGATCGACAGACGCAGACCGAAATCGAACTGTTATTGCGTCACTAACAGAACGTCTTGCGTTTTGTTGTCTTAGCCCCTGGTGTCTGTCAACTTATTAGTG‑‑CGGCGTACCGTTACCGATTTCACCGTAGTTCGCTTCCAGGTATATGTTGTTCGCGTCGTCTCTCAGACCAGTAGCCCa < 2:197417/233‑1 (MQ=255) ccAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGcgtcg < 2:608537/213‑1 (MQ=255) ttcTTCTACGTCTTTGGCTTTAGATTTGGTGGTAGGGATGGAAGGACGTAGACCGAAATCGACCTTGTATTGTGCAACTAACAGGTCGTCTTGCGTTTTGTTAGCGAAGCCGCTGGTGGTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCGCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAg < 1:528504/271‑1 (MQ=255) ttCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCa > 1:437963/1‑274 (MQ=255) tGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCtttttt > 2:206474/1‑191 (MQ=255) tGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGT‑CTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGc > 2:317921/1‑198 (MQ=255) ggacggacGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGT‑‑TCGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCAAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCACACTGTTAACCTTTTTTAACGATGACACGAGGTTGAGATTTTTGCAGGTTGGTACGGTCAGCTGCCCAATAAGGAACAAcaaaacaaaatttgtatctttga > 2:730549/1‑262 (MQ=255) cggacgCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCg < 1:206477/191‑1 (MQ=255) cggacgCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGT‑CTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAag < 1:317924/198‑1 (MQ=255) ggacgCATACTGAAATCGAACGGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTGGGCGAAGCCGCTGGTGTGTGTAAATTTATTAGTG‑‑CGGCGTAGAGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCAGAAGCACCaa < 1:730555/248‑1 (MQ=255) acgCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTcgc > 2:478740/1‑145 (MQ=255) acgCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTcgc > 2:265848/1‑145 (MQ=255) aGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGcgtcg < 1:478743/145‑1 (MQ=255) aGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGcgtcg < 1:265851/145‑1 (MQ=255) aaaTCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTgg > 1:685329/1‑209 (MQ=255) aaCTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGtt > 2:133785/1‑105 (MQ=255) ggTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCt < 1:133786/105‑1 (MQ=255) aCTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTAc > 2:51730/1‑121 (MQ=255) aCTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGATTTTTTACCGTTGCAAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCACCAACGATACCAAAGCCTTCGTATTCGTAGCTGATAGAACCGCCAACACCACCCCCGTTaaaa > 1:730552/1‑274 (MQ=255) aCAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCa < 1:51730/121‑1 (MQ=255) tagcaccggttGCATTTTCTGTGNGAGGCCGTTGGTGTTTGTAATTTTCTTAGTG‑‑GGGCGTAGCTTTCTGGTTTATGCCGTATTGCGCTGACGGGTAGATTTTGTTCGGGTCGTACTGCAGACCAGCAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCACCAACGATACCAAAGCTTTCGTATTCGTAGCTGTTAGACCCGCCAACACCGTCGCCGTTAGTACGGCg < 2:486179/265‑1 (MQ=255) aCGTCTTGCGAAATGTTGGCGAAGCCGCTGGTGTTTGTACATTTATTACTG‑‑CGACGTAGCGTTACGGCTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGGCGTACTTCAGACCAGTAGCCCACTGTTCAGATTTTTTACCGTTGCCAAGAGGTTGAgatactgg > 2:148812/1‑164 (MQ=255) cTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAgg < 1:148813/171‑1 (MQ=255) ttGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTg > 2:129128/1‑166 (MQ=255) gTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAgg < 1:129129/166‑1 (MQ=255) ttgttgGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTATCGTTACGGGTTTCACCGTAGTTCGCTGCAAGGGAGATGTTGTTCGCGTCGTACTTCAGATCAGTAGACCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCAACAACGCTACCAAAGCCTTCGACTTCGTAGCTGATAAAACCGCCAACCCCGTCACCGTTAGAACGGAGTCCaagacccccctgt > 2:806351/1‑262 (MQ=255) tgttgGCGAAGCCGCCGGTGTGTGTAAATTTATTAGTGATCGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGtt > 1:592693/1‑139 (MQ=255) ttgGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCtttt > 1:22870/1‑127 (MQ=255) ggCGAAGCCGCTGGTGTTTGTAAATTGATTAGTGATCGGCGTAGCGTTACTGGTTTCACCGTAGTTCGCTGCCAGGTAGATGGTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTGCTTACCGTTGCCa < 2:592688/139‑1 (MQ=255) cGAAGCCGCTGGTGTTTGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTAc < 2:22870/127‑1 (MQ=255) tGTAAATTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCAc > 2:360817/1‑39 (MQ=255) aaTTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTa < 1:360820/39‑1 (MQ=255) aTTTATTAGTG‑‑CGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGa > 2:49518/1‑78 (MQ=255) || TAGTCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTGATCGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCACCAACGATACCAAAGCCTTCGTATTCGTAGCTGATAGAACCGCCAACACCGTCGCCGTTAGAACGGCGTGCAGTGTCACGCTCG > CP009273/981435‑981890 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |