Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,812,994 A→T 7.4% K24M (AAG→ATG)  PP_3369 → LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,812,9940AT 7.4% 152.2 / 2.9 54K24M (AAG→ATG) PP_3369LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (25/25);  new base T (2/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

AGGCGGGCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGAGCAGATGGCC  >  NC_002947/3812849‑3813142
                                                                                                                                                 |                                                                                                                                                    
aGGCGGGCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCCTTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGAc                                                                                                                                                   <  1:181254/149‑1 (MQ=255)
 ggCGGGCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGAcc                                                                                                                                                  <  6:235167/149‑1 (MQ=255)
   cGGGCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCt                                                                                                                                                <  4:272542/149‑1 (MQ=255)
     ggCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTgg                                                                                                                                              <  8:353829/149‑1 (MQ=255)
      gCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTggg                                                                                                                                             <  1:246207/149‑1 (MQ=255)
           gAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTc                                                                                                                                         <  7:134230/148‑1 (MQ=255)
                      gtgcATAAAGGGGTAGGGTAACCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCAcc                                                                                                                             >  4:57557/4‑149 (MQ=255)
                       gacATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCAcc                                                                                                                             <  6:87222/146‑1 (MQ=255)
                       gTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCATGACCCTGGGTGTCGACCACGCCACCg                                                                                                                            >  4:346531/1‑149 (MQ=255)
                       gTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCATGACCCTGGGTGTCGACCACGCCACCg                                                                                                                            >  4:352301/1‑149 (MQ=255)
                          aTAAAGGGGTAGGGTAACCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTg                                                                                                                                               <  2:328233/127‑1 (MQ=255)
                          aTAAAGGGGTAGGGTAACCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTg                                                                                                                                               >  1:328233/1‑127 (MQ=255)
                                     ccctacccCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCATGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCAt                                                                                                               <  3:346531/148‑1 (MQ=255)
                                     ccctacccCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCATGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCAt                                                                                                               <  3:352301/148‑1 (MQ=255)
                                      cctacccCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCAtcg                                                                                                             >  5:111477/1‑149 (MQ=255)
                                           cccTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGCCCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCGGCTGCCAAGACCCTGGGTGTCGCCCACGCCACCGTGGCCCGGCGCAtcgcttcg                                                                                                        >  4:112580/1‑149 (MQ=255)
                                                      cccGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTc                                                                                             >  7:107873/1‑149 (MQ=255)
                                                       ccGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCg                                                                                            >  6:386668/1‑149 (MQ=255)
                                                              tGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGATCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGc                                                                                     >  7:89917/1‑149 (MQ=255)
                                                                ccGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTc                                                                                         >  6:59049/1‑143 (MQ=255)
                                                                ccGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTc                                                                                         <  5:59049/143‑1 (MQ=255)
                                                                ccGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCt                                                                                    >  2:205408/1‑148 (MQ=255)
                                                                   aGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAg                                                                                >  8:362134/1‑149 (MQ=255)
                                                                    gTCATTAATGTTCGATTTGTAATACCTTCTCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCTCTCGAGGATTCGCTCCAGCTCAAg                                                                                <  8:89917/148‑1 (MQ=255)
                                                                       attcatGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTgg                                                                            >  1:362020/1‑149 (MQ=255)
                                                                        ttcatGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGt                                                                           <  1:15560/149‑1 (MQ=255)
                                                                          catGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTcg                                                                         >  5:135923/1‑149 (MQ=255)
                                                                          catGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTc                                                                          <  7:362134/148‑1 (MQ=255)
                                                                           atGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTcga                                                                        <  5:386668/149‑1 (MQ=255)
                                                                                 gATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTcgaccgac                                                                   <  4:58367/148‑1 (MQ=255)
                                                                                      ggAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGTCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTccc                                                              <  2:362020/148‑1 (MQ=255)
                                                                                      ggAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTcgaccgac                                                                   <  1:118705/143‑1 (MQ=255)
                                                                                      ggAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTcgaccgac                                                                   >  2:118705/1‑143 (MQ=255)
                                                                                          gACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCgcgc                                                         <  8:246172/149‑1 (MQ=255)
                                                                                             cTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTa                                                      >  2:339946/1‑149 (MQ=255)
                                                                                                 gcCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGcc                                                  >  1:223531/1‑149 (MQ=255)
                                                                                                   cATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCt                                                >  4:156379/1‑149 (MQ=255)
                                                                                                    aTTTCTCCGCCTTCAGCTCGGCCGCCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTc                                               >  6:167696/1‑149 (MQ=255)
                                                                                                          ccGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCAc                                         >  1:75539/1‑149 (MQ=255)
                                                                                                            gCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGCCCCTGGGTGTCGACCCCGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCCCg                                        >  5:275434/1‑148 (MQ=255)
                                                                                                            gCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACg                                        >  4:331041/1‑148 (MQ=255)
                                                                                                             ccTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGaa                                      <  6:111477/149‑1 (MQ=255)
                                                                                                              cTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAg                                     <  3:331041/149‑1 (MQ=255)
                                                                                                                tCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGc                                   >  3:311810/1‑149 (MQ=255)
                                                                                                                   gCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCaa                                >  8:849/1‑149 (MQ=255)
                                                                                                                    cTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAAc                               <  1:339946/149‑1 (MQ=255)
                                                                                                                                    tCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTc                 <  6:135923/147‑1 (MQ=255)
                                                                                                                                    tCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGc               >  3:37453/1‑149 (MQ=255)
                                                                                                                                       gctgctGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGa            <  4:311810/149‑1 (MQ=255)
                                                                                                                                       gctgctGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGa            <  2:75539/149‑1 (MQ=255)
                                                                                                                                        ctgctgCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGcc              >  2:84474/1‑146 (MQ=255)
                                                                                                                                           ctgcCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGAGCAg        <  1:205408/149‑1 (MQ=255)
                                                                                                                                            tgcCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACgtgt                           <  8:301550/129‑1 (MQ=255)
                                                                                                                                               cAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGAGCAGATgg    >  8:65056/1‑149 (MQ=255)
                                                                                                                                                 aGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGAGCAGATGGcc  <  7:65056/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
AGGCGGGCATTGAAGCCGGCATGGTCATAAAGGGTTACCCTACCCCTTTATGCACCCGCCACTGCCGAGTCATTCATGTTCGATTGGGAAGACCTGCGCCATTTCTCCGCCTTCAGCTCGGCCGGCTCGCTGTCGGCTGCTGCCAAGACCCTGGGTGTCGACCACGCCACCGTGGCCCGGCGCATCGCTTCGCTCGAGGCTTCGCTCCAGCTCAAGCTGGTCGACCGACGTCCCCGCGCTTATGCCCTCACCCACGAAGGCCAACGTGTTGCGGAACTCGCCGAGCAGATGGCC  >  NC_002947/3812849‑3813142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑