Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,604,685 T→C 11.7% intergenic (‑32/‑96) PP_3179 ← / → PP_3180 LysR family transcriptional regulator/Smp‑30/Cgr1 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,604,6850TC11.7% 128.3 / 7.9 51intergenic (‑32/‑96)PP_3179/PP_3180LysR family transcriptional regulator/Smp‑30/Cgr1 family protein
Reads supporting (aligned to +/- strand):  ref base T (20/25);  new base C (3/3);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

CCGGTTGATCGCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTT  >  NC_002947/3604537‑3604833
                                                                                                                                                    |                                                                                                                                                    
ccGGTTGATCGCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGt                                                                                                                                                      <  3:32464/149‑1 (MQ=255)
 cGGTTGATCGCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTg                                                                                                                                                     <  7:151302/149‑1 (MQ=255)
   gTTGATCGCCTGGCTCAGCGGCGGTTGTGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTACAGCGTGGCGACTCGGCGGCGa                                                                                                                                                    >  5:320016/1‑148 (MQ=255)
               gCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGata                                                                                                                                       <  7:193419/149‑1 (MQ=255)
                    gcggcgGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGa                                                                                                                                         <  8:68904/142‑1 (MQ=255)
                    gcggcgGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGa                                                                                                                                         >  7:68904/1‑142 (MQ=255)
                    gcggcgGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCaaa                                                                                                                                  <  4:317857/149‑1 (MQ=255)
                               gcCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCtt                                                                                                                       >  5:308370/1‑149 (MQ=255)
                                ccATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGCGATATCCATGGGATATCAAAGTTGCATGCttt                                                                                                                      <  2:122864/149‑1 (MQ=255)
                                      gCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAatat                                                                                                                >  4:105775/1‑149 (MQ=255)
                                               gtgCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCAtt                                                                                                       >  2:192759/1‑149 (MQ=255)
                                                         gtgAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttttt                                                                                              <  8:81992/148‑1 (MQ=255)
                                                           gAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgt                                                                                            <  3:306789/148‑1 (MQ=255)
                                                            aaaGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgttg                                                                                          <  5:191509/149‑1 (MQ=255)
                                                                tGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCCATGGATATCacc                                                                                                                                  >  6:45076/1‑103 (MQ=255)
                                                                tGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCCATGGATATCacc                                                                                                                                  <  5:45076/105‑3 (MQ=255)
                                                                   aGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCCATCATCCAGCATTCCTGCAGCGTGGCGACTCGGAGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTTATGatatag                                                                                    >  7:325815/1‑146 (MQ=255)
                                                                           ggCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAgg                                                                           <  6:308370/149‑1 (MQ=255)
                                                                            gCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttttt                                                                                              >  6:46356/1‑129 (MQ=255)
                                                                            gCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttttt                                                                                              <  5:46356/129‑1 (MQ=255)
                                                                            gCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAg                                                                            >  8:197043/1‑147 (MQ=255)
                                                                             ccACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGgag                                                                         <  8:61597/149‑1 (MQ=255)
                                                                               aCGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGaa                                                                       <  4:3801/149‑1 (MQ=255)
                                                                                 ggCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAAtt                                                                     <  1:192759/149‑1 (MQ=255)
                                                                                 ggCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAAtt                                                                     >  4:275187/1‑149 (MQ=255)
                                                                                    gATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTg                                                                    >  4:316950/1‑147 (MQ=255)
                                                                                             ccTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgt                                                                                            >  3:355599/1‑114 (MQ=255)
                                                                                             ccTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgt                                                                                            <  4:355599/114‑1 (MQ=255)
                                                                                             ccTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCAACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgtt                                                                                           >  2:49177/1‑115 (MQ=255)
                                                                                              cTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAg                                                         >  7:81218/1‑148 (MQ=255)
                                                                                              cTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGCGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttt                                                                                                >  2:231145/1‑109 (MQ=255)
                                                                                              cTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGCGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttt                                                                                                <  1:231145/109‑1 (MQ=255)
                                                                                                     atcGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGTCTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAgg                                                                <  4:326776/132‑1 (MQ=255)
                                                                                                     aGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGccc                                                 <  3:105775/149‑1 (MQ=255)
                                                                                                      gCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAAtt                                                                     <  2:304493/128‑1 (MQ=255)
                                                                                                      gCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAAtt                                                                     >  1:304493/1‑128 (MQ=255)
                                                                                                      gCGTGTTTCGATCATCCAGCATTCCTACAGCGTGGCGACTCGGCGGCGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCg                                                <  6:320016/149‑1 (MQ=255)
                                                                                                       cGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGt                                               <  8:81218/149‑1 (MQ=255)
                                                                                                         tgtTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTa                                             <  8:281968/149‑1 (MQ=255)
                                                                                                           tttCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGCGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACt                                           >  2:360107/1‑149 (MQ=255)
                                                                                                               gATCATCCAGCATTCCTGGAGCGTGGCGACTCGGCGGTTATATCCATTGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCAcc                                       <  7:278951/149‑1 (MQ=255)
                                                                                                               gATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCTGAAATGCCAGTTACTccc                                        >  8:278951/1‑146 (MQ=255)
                                                                                                                  catcCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTgg                                    >  1:133922/1‑149 (MQ=255)
                                                                                                                     ccAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGt                                               >  1:211713/1‑135 (MQ=255)
                                                                                                                     ccAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGt                                               <  2:211713/135‑1 (MQ=255)
                                                                                                                       aGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGt                               >  7:92250/1‑149 (MQ=255)
                                                                                                                             ccTGGAGCGTGGCGACTCTGCGTTTATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCt                          <  8:325815/148‑1 (MQ=255)
                                                                                                                              cTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGt                                                                                   <  6:219999/90‑1 (MQ=255)
                                                                                                                              cTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGt                                                                                   >  5:219999/1‑90 (MQ=255)
                                                                                                                                 cAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCtgtg                       <  7:197043/147‑1 (MQ=255)
                                                                                                                                  aGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCa                    <  3:316950/149‑1 (MQ=255)
                                                                                                                                                gcggTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCa      >  7:20053/1‑149 (MQ=255)
                                                                                                                                                    tGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCtt  <  8:20053/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                    
CCGGTTGATCGCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTT  >  NC_002947/3604537‑3604833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑