Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,275,197 A→G 7.4% intergenic (+269/‑23) U712_16850 → / → U712_16855 HTH‑type transcriptional repressor rghR/Hypothetical Protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,275,1970AG 7.4% 160.5 / 4.0 54intergenic (+269/‑23)U712_16850/U712_16855HTH‑type transcriptional repressor rghR/Hypothetical Protein
Reads supporting (aligned to +/- strand):  ref base A (26/24);  new base G (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

GGACGCCAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAATCTCAGCAAATACTTCGA  >  CP006881/3275082‑3275334
                                                                                                                   |                                                                                                                                         
ggACGCCAAAACCCGCCACGATTAAAACACTGGCAGCCGTCCTGCAAGTGCCGTACGAAAACCTAATCGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAACCATCAGAAGGCTAGCAATGCGGTTa                                                                                                                    >  3:254884/1‑139 (MQ=255)
ggACGCCAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGACGCATCTGAAGGCTATCAATCCGTTTa                                                                                                                    >  7:17091/1‑139 (MQ=255)
     ccAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGaaa                                                                                                               <  6:283902/139‑1 (MQ=255)
     ccAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGaaa                                                                                                               <  4:114350/139‑1 (MQ=255)
     ccAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGaaa                                                                                                               <  8:189609/139‑1 (MQ=255)
              gCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTGATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGa                                                                                                      >  7:8856/1‑139 (MQ=255)
              gCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGa                                                                                                      >  1:81123/1‑139 (MQ=255)
              gCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGa                                                                                                      <  8:56540/139‑1 (MQ=255)
                 aCGATTAAAACACTGGCCGCCGGCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCTAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACgg                                                                                                   <  5:259828/139‑1 (MQ=255)
                 aCGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCTAACGAAAACCTATTGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAACAAACCCCCGAACCATCTGAATGATATCAATCCGTTTATGAAATTTACCAGACgg                                                                                                   <  5:268329/139‑1 (MQ=255)
                 aCGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTACTGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACgg                                                                                                   <  8:368026/139‑1 (MQ=255)
                        aaataatGGCAGCCGTCATGAAAGTGACGTAGTAAAAACTAATGGCCTCCGATGGCCATATTCAGGCCTTTCATGATTTAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACTGCTGTcac                                                                                            <  8:151199/133‑1 (MQ=255)
                           accTGGCAGCCGTCCTGAATGGGCCGTACGAAAACCTAAAGGCCGCCGCAGGCCATATTCAGGCCTTACCTGAAGAAATCCGCGAACCATCTGAAGGCTATCAATCCGTTTCTGAAATTTACCAGACGGCTGTCACAcg                                                                                         <  7:219305/137‑1 (MQ=255)
                           accTGGCAGCCCGCCTGAAAGTGCCGTACGAAAACCTACTGGCCGCCGCAGGCCATATTCAGGCCTTTCCTCAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGATTATGAAATTTACCAGACGGCTGTCACAcg                                                                                         <  3:41071/137‑1 (MQ=255)
                           aaCTGGCCGCCGGCCTGAACGTGCCGTACGAAAACCTAATGGAGGCCGCAGGCCATATTCAGGCCTTACCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACAcg                                                                                         <  1:271817/139‑1 (MQ=255)
                               ggCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACAcgcg                                                                                       >  7:166476/1‑137 (MQ=255)
                               ggCAGCCGTACTGAAACTGCCGTACGAAAACCTAATGGCCGCCGCACGCCATATTCAGGCCTATCCTGAAGAAATCCGCGAAGCATCTGAAGGCGAACAATCCGTTTATCAAATATACCAGACGGCTCTCACAcgcg                                                                                       >  2:243417/1‑137 (MQ=255)
                                gCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTGTCCTGAAGAAATCCGCGAAGCATCGGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACgcggag                                                                                    <  7:247993/139‑1 (MQ=255)
                                gCAGCCGCCAGGAAAGTGCCTTACGAAAACCTACTGGCCGCCGCAGGCAATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACgcggag                                                                                    <  7:320078/139‑1 (MQ=255)
                                 cAGCCGGCCTTAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTTAAGAAATCCGCTAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACgcggagc                                                                                   <  5:259211/139‑1 (MQ=255)
                                            aaaGGGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTcc                                                                        <  5:18486/139‑1 (MQ=255)
                                             aaGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTcc                                                                        <  2:324338/138‑1 (MQ=255)
                                                 gCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGAtt                                                                   >  1:225722/1‑139 (MQ=255)
                                                  ccGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACAAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGAttt                                                                  >  6:110823/1‑139 (MQ=255)
                                                   cGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACAcgcg                                                                                       >  7:250522/1‑117 (MQ=255)
                                                   cGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACAcgcg                                                                                       <  8:250522/117‑1 (MQ=255)
                                                                             ggCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACAtctct                                       <  8:8856/139‑1 (MQ=255)
                                                                             ggCAATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACAtctct                                       <  2:204614/139‑1 (MQ=255)
                                                                                  tatTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  >  5:69672/1‑139 (MQ=255)
                                                                                   atTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  >  1:268743/1‑138 (MQ=255)
                                                                                   atTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACCGCTGTCACACGCGGAGCGGAGCACCTACCGATTTTCAAAACTCAAAAATGGGAACATCTCTCAAAg                                  >  2:145722/1‑138 (MQ=255)
                                                                                         gCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGACCATCTCTCAAAGCAGGata                           >  4:300753/1‑139 (MQ=255)
                                                                                            tttCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  <  5:342908/129‑1 (MQ=255)
                                                                                            tttCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  >  6:342908/1‑129 (MQ=255)
                                                                                             ttCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGCCGGCTGTCCCACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAGGCAGGATATTg                        >  3:86043/1‑138 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCGTCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGa                       >  7:203536/1‑138 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCGTCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGa                       >  7:208777/1‑138 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATc                                                                                                                          >  1:75334/1‑39 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATc                                                                                                                          <  2:75334/39‑1 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCa                                                                                                        <  7:15173/57‑1 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCa                                                                                                        >  8:15173/1‑57 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAACGCAGGATATTGa                       >  2:189523/1‑138 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  >  1:278598/1‑127 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAg                                  <  2:278598/127‑1 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCa                                >  6:236880/1‑129 (MQ=255)
                                                                                              tCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCa                                <  5:236880/129‑1 (MQ=255)
                                                                                               ccTGAAGAAATCCGCGAAGCGTCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGaa                      <  8:203536/138‑1 (MQ=255)
                                                                                               ccTGAAGAAATCCGCGAAGCGTCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGaa                      <  8:208777/138‑1 (MQ=255)
                                                                                                   aagaaATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAAtct                 >  7:314602/1‑139 (MQ=255)
                                                                                                   aagaaATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAAtct                 >  5:124300/1‑139 (MQ=255)
                                                                                                   aagaaATCCGCGAAGCATCTGAACTCTATAAAAACGTTTATCAAATTTAACAGACGGCTGTCACACGAGGAGCGGAGCACATCCCGATTTTAAAAAGTCAAAAATGGCAACATCTCTCAAAGCAGGATATTGAAAAtct                 >  7:68945/1‑139 (MQ=255)
                                                                                                        aTCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAATCTAAGc             >  3:157442/1‑138 (MQ=255)
                                                                                                         tCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAATATGGGAACATCTCTCAAAGCAGGATATTGAAAATCTCAGCa            >  5:129402/1‑138 (MQ=255)
                                                                                                                  cATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAATCTCAGCAAATACTTCGa  >  4:254119/1‑139 (MQ=255)
                                                                                                                   |                                                                                                                                         
GGACGCCAAAACCCGCCACGATTAAAAAACTGGCAGCCGTCCTGAAAGTGCCGTACGAAAACCTAATGGCCGCCGCAGGCCATATTCAGGCCTTTCCTGAAGAAATCCGCGAAGCATCTGAAGGCTATCAATCCGTTTATGAAATTTACCAGACGGCTGTCACACGCGGAGCGGAGCACCTCCCGATTTTCAATAGTCAAAAATGGGAACATCTCTCAAAGCAGGATATTGAAAATCTCAGCAAATACTTCGA  >  CP006881/3275082‑3275334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑