| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 3,207,739 | A→C | 100% | D445A (GAT→GCT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 3,207,739 | 0 | A | C | 97.3% | 125.0 / ‑3.6 | 37 | D445A (GAT→GCT) | rpoD | RNA polymerase, sigma 70 (sigma D) factor |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (18/18); total (18/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.48e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
TCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGC > CP009273/3207487‑3207915 | tCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCCCAGGCGCGCACCATCCGTAtt > 1:64490/1‑275 (MQ=255) cgtagtATGTCCATCGGTGAAGCGAAAGCCAGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCg < 1:235401/273‑1 (MQ=255) ttATGTCCATANGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCat < 2:64490/274‑1 (MQ=255) gCGAAAGCCCTCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATcaa < 1:390831/275‑1 (MQ=255) aGCGAACTTTCGTCTGGTTATGTATAGCGCTAAGAAAGACACCAACCGTGGCTTGCAGTGACTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAAGTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATAGGATTGAGACCATCAACAAGCt < 1:110991/246‑1 (MQ=255) cTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGCTGGATCAGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTTACACCATCCACAAGCTCAAc > 1:9384/1‑244 (MQ=255) tCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGAAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGCTCACCCGCTCTNTCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTtctc > 1:761373/1‑234 (MQ=255) aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCTAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTAt > 2:647699/1‑169 (MQ=255) aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTAt > 2:69645/1‑169 (MQ=255) aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGACTCAGgcgc > 1:709974/1‑156 (MQ=255) tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc < 2:709966/156‑1 (MQ=255) tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCg < 1:69645/169‑1 (MQ=255) tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGAGCGCACCATCCGTATTCCg < 1:647706/169‑1 (MQ=255) cAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTAGTCACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCTGGCGACCACCCGCCTTATCGCGGCTCCGGCGCGCACCATCCGTATTCCGGTGCATATGATAGAGACCATCCACAAGCCCAACCGGATTTCTCCCCAGATACTGCACGAACTGGGCCGTGAACCGCCGCCTGAAGAACTGGCGGAACGCCGGCGGATGCAGGa > 2:211479/1‑275 (MQ=255) aTTCAGGAAGTCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCa < 1:211482/274‑1 (MQ=255) tgcaccctCGTTCTCATAAAAGCGTTTGTTATCTTCGTATACCGCCGTTGTTACAACTTCTCCACCTACGCAACCTGGTTGCTCCGTCAGGCTATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATTGTCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGaa < 1:410889/268‑1 (MQ=255) gCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCAGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCAAGATGCTGCAAGAGATGGGCCGTGAACCTACGCCGGAAGAACTGGCTGACCGTATGCTGATGCCGGAAAACAAGAACCGAAACATGCTGAAg > 1:253796/1‑275 (MQ=255) atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCCGGCGCGCACCATCCGTACTCCGGTGCATATGATTGACACCATCAACAAGATCAACCGCATTTCTCGCCAGATCCTGCAAGAGATGGCCAGTCACCCGACCCACGAAGAACTGTCTGAACGCATGCTCATTACGCAGGACAAGATCCGCAAAGTCCTAAGTATCGccctagtct > 2:127451/1‑267 (MQ=255) ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCa > 1:538274/1‑132 (MQ=255) tAAATTCGAATCCCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATcaa < 2:538269/132‑1 (MQ=255) cgccgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTg > 1:497728/1‑99 (MQ=255) gTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCata < 2:497723/99‑1 (MQ=255) tACAAGTGCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCTGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCa < 1:792114/214‑1 (MQ=255) ctcCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgc > 2:131247/1‑62 (MQ=255) aCCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc < 1:131247/62‑1 (MQ=255) tggATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCa > 1:7004/1‑46 (MQ=255) tCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAcctt < 2:7004/46‑3 (MQ=255) ccGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGa > 1:648861/1‑191 (MQ=255) ccGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCACCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGa > 1:522895/1‑168 (MQ=255) cAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATg > 1:414445/1‑159 (MQ=255) cAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGAt < 2:648854/191‑1 (MQ=255) cAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCACCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGAc < 2:522890/168‑1 (MQ=255) cGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTAGTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCgg < 2:414440/159‑1 (MQ=255) aCCCGCTCTATCGCGACTCAGGCATGCATCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGAt > 1:581025/1‑149 (MQ=255) cccGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGAt < 1:187451/91‑1 (MQ=255) gCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCg < 2:581020/149‑1 (MQ=255) gcgGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAgaga > 1:686287/1‑91 (MQ=255) | TCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGC > CP009273/3207487‑3207915 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |