Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,480,130 T→C 8.4% intergenic (+19/‑20) crp → / → yhfK cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein, tandem domains

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,480,1300TC 8.4% 114.7 / 3.6 54intergenic (+19/‑20)crp/yhfKcAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein, tandem domains
Reads supporting (aligned to +/- strand):  ref base T (32/16);  new base C (2/3);  total (35/19)
Fisher's exact test for biased strand distribution p-value = 3.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.65e-01

CCGTCAGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGATTCGGTCT  >  CP009273/3479985‑3480274
                                                                                                                                                 |                                                                                                                                                
ccGTCAGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGGTAATACCGTCGGAGTGGCGCGTTAc                                                                                                                                               >  1:619142/1‑149 (MQ=255)
  gTCAGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCt                                                                                                                                             >  1:629569/1‑149 (MQ=255)
     aGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGGGGCGCGTTCCCTGGt                                                                                                                                          >  1:1097744/1‑149 (MQ=255)
           ttGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAAACTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGCAGGCATGGGGCGCTCCCTGGTAccgcg                                                                                                                                    >  2:123585/1‑149 (MQ=255)
            tGGTCAGATTGTCGGCTGTTCTCCTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGCTACCAGGTAacgcgc                                                                                                                                   <  2:540476/149‑1 (MQ=255)
              gTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGCTACCAGGTAACGCGCCa                                                                                                                                 <  1:769905/149‑1 (MQ=255)
              gTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGCTACCAGGTAACGCGCCa                                                                                                                                 <  1:50163/149‑1 (MQ=255)
                cAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCAtt                                                                                                                               <  1:880158/149‑1 (MQ=255)
                cAGATTGCCGGCTGTTCTCGTGAACGCGTGGGACGCATTCTGACGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGGTAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCAtt                                                                                                                               <  1:761479/149‑1 (MQ=255)
                 aGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATGAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGGGGAGGGTTACCTGGTCGCGCGGCactg                                                                                                                              >  1:281271/1‑146 (MQ=255)
                 aGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTCCCTGGGAGCGCGCCAttt                                                                                                                              >  1:1059650/1‑149 (MQ=255)
                    ttGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTGTACGGCACTCGTTGGTCCCGACGGAGTGTCGCGTTATCTCGTATGCCGCCATTTTGt                                                                                                                           >  1:566524/1‑149 (MQ=255)
                             gTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGa                                                                                                                  >  1:1003587/1‑149 (MQ=255)
                             gTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGGAGCGCGCCCTTTTGTTTCCCCCGa                                                                                                                  >  2:370885/1‑149 (MQ=255)
                             gTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTGACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCgc                                                                                                                  >  2:925671/1‑148 (MQ=255)
                                   gggAATCCGTGGCACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGgc                                                                                                            <  2:95506/147‑1 (MQ=255)
                                          cGTGGGACGCATTCTGAAGATGCTGGAAGATAAGAACCTGATCTCCGCACACGGTAAAGCCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTAACTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGAAGACt                                                                                                     >  2:5927/1‑149 (MQ=255)
                                              ggACGCATTCTGAACATCCTCGAAGATCAGAACCTGACCTCCGCACACGGTAAAACCATCGTCCTTTACGGCACTCCTCAATCCCGTCGCAGTGGCCCGTTACCGGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGAtt                                                                                                 <  2:246689/149‑1 (MQ=255)
                                                aCGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAACCCATCGTCGTTTACGGCACTCGTTAATCCCGCCGGAGTGGCGCGTTACCTGGTAGCACGCCATGTTGTTTCCCCCGATGTCGCGCAGACTGAttca                                                                                               >  2:612211/1‑147 (MQ=255)
                                                     ttCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGCTTTATCAcc                                                                                          >  1:233048/1‑149 (MQ=255)
                                                      tCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGGACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCAccc                                                                                         >  1:807159/1‑149 (MQ=255)
                                                       cTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCAcccc                                                                                        >  1:1188438/1‑149 (MQ=255)
                                                        tGAAGATGCGTGGAGAGCGGAACCTGATCGCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGGCGGAGTGGCGCGTTACCTGGTAGCGCGTCATTTTGTTGCCCCCGATGTGGCGCAGACTGATTTATCACCCCg                                                                                       <  2:541791/149‑1 (MQ=255)
                                                         gAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACCGCTTTATCACCCCgg                                                                                      >  2:375167/1‑148 (MQ=255)
                                                           aGATGCTGGAAGGTCAGAACCTGATCTCCGCACACGGTAAAGCCATCGTCGTTGACGGCACTCGGTAATCCCGGCGGGGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCGGCCTGAGTTATCAGCCCGatg                                                                                    >  2:622242/1‑148 (MQ=255)
                                                             aTGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCCGACTGATTTATCACCCCGGTATc                                                                                  >  1:38985/1‑149 (MQ=255)
                                                             aTGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATc                                                                                  <  1:994735/149‑1 (MQ=255)
                                                                  ggAAGATCAGCACCTGTTCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTa                                                                             <  1:1012817/149‑1 (MQ=255)
                                                                  ggAAGATCAGACCCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTa                                                                             <  1:698699/149‑1 (MQ=255)
                                                                   gAAGATCAGAACCTGGTCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGCTTGATCGCCCCGATATCAACTAt                                                                            >  2:688802/1‑149 (MQ=255)
                                                                        tCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGGTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCCGACGGATTTATCACCCCCATGTCAACTAGTCACt                                                                       >  1:430778/1‑149 (MQ=255)
                                                                              ccTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACa                                                                 >  1:969406/1‑149 (MQ=255)
                                                                               cTGATCTCCGCACACGGTCAAGCCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACaa                                                                <  1:1083961/149‑1 (MQ=255)
                                                                                   tctcCGCACACGGTAAAACCATCGTCGTCTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGc                                                            <  1:824807/149‑1 (MQ=255)
                                                                                        gCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGGTTTATCACCCCGCTATCAACTATGCACTTCCACAAACGCTGGTg                                                       >  1:128328/1‑149 (MQ=255)
                                                                                                      cATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGt                                         >  1:1209957/1‑149 (MQ=255)
                                                                                                      cATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTAGGTTTGCCCGt                                         >  1:161525/1‑149 (MQ=255)
                                                                                                        tcgtcgTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTTCCCGTgg                                       >  1:1078492/1‑149 (MQ=255)
                                                                                                           tcgtTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCg                                    >  1:885696/1‑149 (MQ=255)
                                                                                                               ttACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTgg                                >  2:1227809/1‑149 (MQ=255)
                                                                                                                 aCGGCGCTCGTTAATCCCGGCGGAGTGGCGCGTTACCTGGTGGCGCGCCGTTTTGTTTCCCGCGATGTGGCGCAGTCTGATTTATCGTCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGt                              <  2:473192/149‑1 (MQ=255)
                                                                                                                  cggaccttcgtagtCCCGTCGGGGGGGCGCGTTACCTGGTATCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGtt                             <  2:241758/136‑1 (MQ=255)
                                                                                                                    gCACTGGCTAGTCCCGTCGGGGTGGCGCGTTACCTGGTATCGCGCCATTTTGTTTCCCCCGATATGGCGCAAAGGTATCTCTCACCCCGAAATCAACTATGCACTTCGACAAACGCTGGGGCTATGTTTGCCCGTGGCCGTTGGGTTaa                           <  2:752419/149‑1 (MQ=255)
                                                                                                                     ccgtcggtgaTCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCTGATGTGGCGCAGGCTGATTTATCACCCCCATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAAt                          <  2:433527/140‑1 (MQ=255)
                                                                                                                               tCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGGCAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGaa                >  1:1191738/1‑149 (MQ=255)
                                                                                                                               tCCCGCCGGAGTGGCGCGTTACCCGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGCTATCAACTATGCACTTCGACTAACGCTGGTGCCATGTTTGCCCGCGGCCGTCGGGCTAATCCTTGGCCaa                >  2:811869/1‑149 (MQ=255)
                                                                                                                                     cGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGACTTACGa          >  2:1163422/1‑149 (MQ=255)
                                                                                                                                       aaatGGCGCGCTACCAGGTAACGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGAtt        >  2:906689/4‑149 (MQ=255)
                                                                                                                                         ggggCGCGTTACCGGGGAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGATTCg      <  2:139869/147‑1 (MQ=255)
                                                                                                                                           ggCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGGCTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTTTTTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAGTTCCGATTCGGt    >  1:932538/1‑149 (MQ=255)
                                                                                                                                            tcgcgTGCCCTGGTATCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACTCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGATTCGGTc   <  2:446667/148‑1 (MQ=255)
                                                                                                                                            gcgcGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAGCGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGCGGAATTACGATTCGGTc   >  2:45105/1‑149 (MQ=255)
                                                                                                                                            gcgcGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCGGTGGCCGTTGCGTTAATGCTTGGGGCATTAAGAGTAGGtt   >  1:1146475/1‑148 (MQ=255)
                                                                                                                                             cgcgTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGATTCGGTCt  >  2:1051720/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
CCGTCAGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAATCCCGTCGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTGTTTCCCCCGATGTGGCGCAGACTGATTTATCACCCCGATATCAACTATGCACTTCGACAAACGCTGGTGCTATGTTTGCCCGTGGCCGTTGGGTTAATGCTTGGCGAATTACGATTCGGTCT  >  CP009273/3479985‑3480274

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑