| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 1,184,046 | T→G | 100% | E396A (GAG→GCG) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 1,184,046 | 0 | T | G | 93.3% | 131.6 / ‑1.4 | 40 | E396A (GAG→GCG) | phoQ | sensory histidine kinase in two‑component regulatory system with PhoP |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base G (19/18); total (20/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
ATTTTACCCTCATATTGCTCGGTGATTTCGCGGGCTACCGCCAGCCCTACACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACTCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATAC > CP009273/1183854‑1184256 | aTTTTACCCTCATATTGCTCGGTGATTTCGCGGGCTACCGCCAGCCCTACACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAatat > 2:399269/1‑204 (MQ=255)aTTTTACCCTCATATTGCTCGGTGATTTCGCGGGCTACCGCCAGCCCTACACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACATCAACAAAATCGTTCTGCTAACCAAAAAAGCTGAtctc > 1:366287/1‑275 (MQ=255) tACCCTCATATTGCTCGGTGATTTCGCGGGCTACCGCCAGCCCTACACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTAc < 1:399274/204‑1 (MQ=255) ttctgcgttGATGTCGCGCGCTACCCCCAGCCCTCCGCCTTGCCCAGGGCGTAAAGTAGCTACCGTTTAACCACAGTCGAAAATGACCTCTCGCTTGCTTAATGGAATCCCGGGGCCATCATCCCCGACCACAATATAGGGATGCTCGTCGGTTTGCCTTGCAGAAAGTTCGACAAACGAGAGGCAATATTTACAGGCAATATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATc < 2:788691/265‑1 (MQ=255) gTGATTTCGCGGGCTACCGCCAGCCCTAAACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTAGACAAACGCGAGGCAATATNTACAGGCATTATCCAGCACGTTGCCCATCACATCGACAAAATCGTTCTGCTCACCGACAAAGCAGATCTATGGCGAAATATCgagagag > 1:631346/1‑273 (MQ=255) tcccTAACCCGTGCCCAGGGCGTAAAGTCTCCACCCCTGACCCACGGTAGAAACTTCCCTCTCGCTTGCTTAATTGCATCCCGGGGCCATCATCCTTGTCCACAATCTCGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCCCGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGAt < 2:366282/272‑1 (MQ=255) tACACCTTGCCCAGGGCGTATAGTATCAACCCGTTTACCACGGTCGAAAATGACCTCTCGCTTTCTTAATGGAATACCTGGTCCATCATCCTCGCCCATAATATAGAGATGCTCGTCGGTTTTCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGTCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACt < 1:674253/274‑1 (MQ=255) cacCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACACAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGaaa > 1:400712/1‑234 (MQ=255) tCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGt > 1:251975/1‑274 (MQ=255) cAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACa > 2:125854/1‑136 (MQ=255) ccGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCa < 1:125854/136‑1 (MQ=255) gACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGaaa > 1:329275/1‑201 (MQ=255) tccACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACTCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTCAGATTGTCCAGCAGTgggg < 1:653364/274‑1 (MQ=255) gtcGGTCGAAAATGACCTCGCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCAAAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTgggg < 2:251971/271‑1 (MQ=255) aaTGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTGCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAAt > 1:138683/1‑273 (MQ=255) ggggCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATg < 1:390202/243‑1 (MQ=255) gggCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACTCGa > 1:195396/1‑70 (MQ=255) gggCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGt > 2:376359/1‑228 (MQ=255) gCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCATTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTAGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGGGCGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCGGGGCAAGGGcccccccctaatcc > 2:759975/1‑267 (MQ=255) catcatCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACTCGAGGCa < 2:195393/70‑1 (MQ=255) catcatCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTgggg < 1:376364/228‑1 (MQ=255) catcCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTc > 2:164495/1‑214 (MQ=255) cTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCcagc < 1:164495/214‑1 (MQ=255) caATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAAcgcg > 2:490948/1‑50 (MQ=255) ataGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGc < 1:490953/50‑1 (MQ=255) tGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAatat > 2:200922/1‑48 (MQ=255) tGCTCGTCGGCTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTAGAGGCATTATCTAGCACGTTCCCCATCACCTCGACAAAAta > 2:670123/1‑91 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGCCAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGt > 2:170399/1‑154 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGa > 1:743983/1‑113 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGa > 2:239480/1‑123 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAata > 1:779960/1‑127 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCg > 1:428530/1‑130 (MQ=255) cTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAg > 2:290953/1‑213 (MQ=255) cgtcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAAGATTTAc < 1:200925/48‑1 (MQ=255) cgacgGTTTGCCTTGCGGAAATTTCGACAAACGCGAGGCAATATTTACAAGCATTATCCAGCACGTTGCCCATCACCGCGACAAAATCGTTc < 1:670130/89‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGAtctc < 2:743975/113‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAata < 1:239484/123‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCgagag < 2:428525/130‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCga < 2:779951/127‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGAt < 1:170399/154‑1 (MQ=255) tcgGTTTGCCTTGCAGAAATTTCGACAAACGCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTcg < 1:290957/213‑1 (MQ=255) | ATTTTACCCTCATATTGCTCGGTGATTTCGCGGGCTACCGCCAGCCCTACACCTTGCCCAGGGCGTAAAGTATCAACCCGTTGACCACGGTCGAAAATGACCTCTCGCTTGCTTAATGGAATACCGGGGCCATCATCCTCGACCACAATATAGAGATGCTCGTCGGTTTGCCTTGCAGAAATTTCGACAAACTCGAGGCAATATTTACAGGCATTATCCAGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATAC > CP009273/1183854‑1184256 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |