Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 1,191,748 C→T 10.4% T390T (ACC→ACT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092731,191,7480CT10.4% 145.4 / 2.8 54T390T (ACC→ACT) icde14 prophage; isocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base C (28/20);  new base T (4/2);  total (32/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTG  >  CP009273/1191601‑1191891
                                                                                                                                                   |                                                                                                                                               
ggcgcCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCAGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACATAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAcccc                                                                                                                                                >  2:18761/2‑148 (MQ=255)
    ccGAAATATGCCGGTCAGGACAAAGTTAATCCTGGCTCTATTATACTCTCCTCTGAGTGGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGa                                                                                                                                            <  1:711401/149‑1 (MQ=37)
    ccGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGCTCGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTACCTTATGa                                                                                                                                            >  2:751610/1‑149 (MQ=18)
            tGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGCATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                                                                                                    >  1:1019743/1‑149 (MQ=255)
               cGGTCAGGACAAAGTAAATCCTGGCTCTATTATTTTCCCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTc                                                                                                                                 <  1:29543/149‑1 (MQ=255)
                ggTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGATGCGTCAAATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt                                                                                                                                >  1:852845/1‑149 (MQ=17)
                  tcaggcatacgTAAGTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga                                                                                                                              >  2:1134859/11‑149 (MQ=255)
                      gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                                                                                                          <  1:1134163/149‑1 (MQ=255)
                         aaactcaaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                                                                                                       <  2:221490/143‑1 (MQ=255)
                         aaaGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTTCGCCACATGGGTTGGTCCGAAGCGGCAGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAGCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                                                                                                       <  2:481477/149‑1 (MQ=255)
                         aaaGGAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAATCCGTAACCTATGACTTCGAGCGTCTGatggatgg                                                                                                                       <  1:688157/149‑1 (MQ=255)
                           aGTAAGTCCTGGCTCTGTTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcg                                                                                                                     <  2:583801/149‑1 (MQ=11)
                           aGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcg                                                                                                                     <  2:707350/149‑1 (MQ=11)
                            gTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcgc                                                                                                                    >  1:1093492/1‑149 (MQ=11)
                               aaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                                                                                 >  1:1179295/1‑149 (MQ=255)
                                aTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                                                                                >  1:1067930/1‑149 (MQ=255)
                                      gCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTAGAACGTCTGATGGAAGGCGCTAAGctgctg                                                                                                          >  1:368566/1‑149 (MQ=11)
                                          tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGGTGGCGCTAAACTGCTGGAAt                                                                                                      >  2:178273/1‑149 (MQ=255)
                                          tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                                                                                                      <  1:110620/149‑1 (MQ=255)
                                           attattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTCAACGGCTGAAATg                                                                                                     >  2:528477/1‑149 (MQ=255)
                                              attCTCTCCGCTGAGATGATGCCGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTc                                                                                                  <  1:953126/149‑1 (MQ=255)
                                                   ctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGt                                                                                             >  2:935628/1‑149 (MQ=255)
                                                               gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTACACTGATAAAATGATAAGAGTTTGGTGACGCGa                                                                                 >  1:224367/1‑149 (MQ=18)
                                                               gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGATTGGTGAggcgc                                                                                 >  1:278578/1‑148 (MQ=255)
                                                                atgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat                                                                                <  1:351126/149‑1 (MQ=255)
                                                                  gctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca                                                                              >  2:835479/1‑149 (MQ=255)
                                                                    tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc                                                                            >  1:1008762/1‑149 (MQ=255)
                                                                       gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                                         >  2:1150048/1‑149 (MQ=255)
                                                                                gTTGGACCGAAGCGGCTGACTTAATTGTTAACGGTATGGAAGGCGCAACCACCGTGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                                                                <  2:1147048/149‑1 (MQ=255)
                                                                                 ttGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAAAGTTTGGTGACGCGATCATCGAAAACATGTAAt                                                               >  1:1059390/1‑149 (MQ=255)
                                                                                  tGGACCGAAGCGGCTGACTTAAGTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATg                                                              <  1:645801/149‑1 (MQ=255)
                                                                                      ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt                                                          >  1:941991/1‑149 (MQ=255)
                                                                                       ggtaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTa                                                         <  2:924384/146‑1 (MQ=255)
                                                                                                tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGGCGCGATCATCGAAAACATATAATGCCGTAGTTTGTTaa                                                >  2:473723/1‑149 (MQ=255)
                                                                                                tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaa                                                >  2:509939/1‑149 (MQ=255)
                                                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAACCCGTAACCTCTGACTTCAAGCGTCTGATGGATGGCGCTAAGCAGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                                            >  1:247936/1‑149 (MQ=18)
                                                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGGGCGTCTGATGGATGGCGCTAAACTGCGGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGGAATGCCGTAGTTGGTTAAAttt                                            >  1:290196/1‑149 (MQ=255)
                                                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                                            >  1:458122/1‑149 (MQ=255)
                                                                                                    ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                                            >  2:548050/1‑149 (MQ=255)
                                                                                                       aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttatt                                         <  1:848477/149‑1 (MQ=255)
                                                                                                           tcaaaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCCGAGTTTGGTGACGCGAGCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACg                                     <  2:869738/147‑1 (MQ=255)
                                                                                                                 gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGGAGACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCg                               >  2:379561/1‑149 (MQ=255)
                                                                                                                  tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTTTTAACGGGAGCGt                              >  1:995298/1‑149 (MQ=255)
                                                                                                                   aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGGTAGATTGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTa                             >  1:853817/1‑149 (MQ=255)
                                                                                                                    tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTaa                            <  1:587820/149‑1 (MQ=255)
                                                                                                                    tGGAAGGCGCAACCACCGCGAAAACCGTAACCTATGACCTCGAGCGTCTGATGGCTGGCGTTAAACTGCAGAAATGTTCAGCGGTTGGTGACGCGACCAGCGAAAACACGTAATGCCGTAGATTGTTAAATTTATTAACGGGAGCGTaa                            <  2:958540/149‑1 (MQ=255)
                                                                                                                                     gcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGtttttt           >  2:1167798/1‑149 (MQ=255)
                                                                                                                                       gAAAACCGTAACCTATGAAATCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGt         >  2:455401/1‑149 (MQ=255)
                                                                                                                                        aaacCCGTAACCTATGACTTCTAGCGTCTGATGGATGGCGCAAAACTGGTAAAATCTTCAGAGTTTGGCGTCGCAATCAGCGCAAACCTCTAATGCCATAGTTTGGTAAATTACTTAACGGGAACGTAACGCTCCCGTGGTTTTTTGta        <  2:490354/149‑2 (MQ=255)
                                                                                                                                         aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTa       >  1:1086060/1‑149 (MQ=255)
                                                                                                                                         aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAAAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTa       <  2:1059390/149‑1 (MQ=255)
                                                                                                                                         aaaCCGTAACCTATGACTTCGAGCGTCTGAGGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTCGTTAGATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTa       >  2:938220/1‑149 (MQ=255)
                                                                                                                                             cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTCAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgct   <  1:1223143/149‑1 (MQ=255)
                                                                                                                                             cGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAGGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgct   >  1:610234/1‑149 (MQ=255)
                                                                                                                                              ttAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgctg  <  1:505988/148‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                               
TGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTG  >  CP009273/1191601‑1191891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑