Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,277,323 C→A 7.1% G16V (GGT→GTT)  PP_1116 ← resolvase family site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,277,3230CA 7.1% 168.5 / 3.8 56G16V (GGT→GTT) PP_1116resolvase family site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base C (25/27);  new base A (2/2);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01

TGTCAGAGCTTTTGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAATTCTAGATTTCC  >  NC_002947/1277175‑1277469
                                                                                                                                                    |                                                                                                                                                  
tGTCAGAGCTTTTGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCAc                                                                                                                                                    >  5:180263/1‑149 (MQ=255)
 gTCAGAGCTTTTGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCAc                                                                                                                                                    <  6:133692/148‑1 (MQ=255)
     gagCTTTTGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGa                                                                                                                                               >  4:146540/1‑149 (MQ=255)
         ttttGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGActct                                                                                                                                           >  1:127275/1‑149 (MQ=255)
         ttttGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGActct                                                                                                                                           >  7:124396/1‑149 (MQ=255)
          tttGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCtt                                                                                                                                          >  6:277201/1‑149 (MQ=255)
            tGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTg                                                                                                                                         <  6:5788/148‑1 (MQ=255)
             gCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTgg                                                                                                                                        <  2:167140/148‑1 (MQ=255)
              cACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGt                                                                                                                                       <  7:143447/148‑1 (MQ=255)
              cACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGt                                                                                                                                       <  5:277201/148‑1 (MQ=255)
                       gACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGa                                                                                                                                    <  6:112064/142‑1 (MQ=255)
                       gACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGa                                                                                                                                    >  5:112064/1‑142 (MQ=255)
                        aCGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGaa                                                                                                                            <  8:124396/149‑1 (MQ=255)
                         cGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAAt                                                                                                                           <  3:154489/149‑1 (MQ=255)
                          gATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATg                                                                                                                          >  2:188846/1‑149 (MQ=255)
                                cAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGc                                                                                                                     >  8:99121/1‑148 (MQ=255)
                                 aaGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGcaa                                                                                                                   <  6:180263/149‑1 (MQ=255)
                                          cTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTg                                                                                                          <  1:14077/149‑1 (MQ=255)
                                               ccGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCat                                                                                                      >  1:19615/1‑148 (MQ=255)
                                               ccGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCat                                                                                                      >  5:99656/1‑148 (MQ=255)
                                                cGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCatga                                                                                                    <  8:204948/149‑1 (MQ=255)
                                                   tACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTc                                                                                                        <  6:4081/142‑1 (MQ=255)
                                                   tACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTc                                                                                                        >  5:4081/1‑142 (MQ=255)
                                                      cacaTCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATgg                                                                                              >  5:137184/1‑149 (MQ=255)
                                                       acaTCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGa                                                                                                                             >  4:245507/1‑117 (MQ=255)
                                                         aTCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGActct                                                                                                                                           <  2:269061/101‑1 (MQ=255)
                                                             acaAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCt                                                                                       >  3:186885/1‑149 (MQ=255)
                                                             acaAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCt                                                                                       >  3:208443/1‑149 (MQ=255)
                                                              caAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTc                                                                                           <  3:185198/144‑1 (MQ=255)
                                                              caAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTc                                                                                           >  4:185198/1‑144 (MQ=255)
                                                                       cAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCAAGGTGActc                                                                                                                                            <  4:153211/86‑1 (MQ=255)
                                                                       cAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCAAGGTGActc                                                                                                                                            >  3:153211/1‑86 (MQ=255)
                                                                                   aGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCaa                                                                 <  6:137184/149‑1 (MQ=255)
                                                                                    gTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAAc                                                                <  1:188846/149‑1 (MQ=255)
                                                                                        ttCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGc                                                             >  6:101331/1‑148 (MQ=255)
                                                                                        ttCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGc                                                             >  6:281326/1‑148 (MQ=255)
                                                                                             ttGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAg                                                       >  6:280343/1‑149 (MQ=255)
                                                                                                    gCACGTTGGATGTAATCACGCTGGGCTTCCCGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTg                                                 >  1:141570/1‑148 (MQ=255)
                                                                                                            taTGTAATCACGCTGGGCTTCCAGTCCTAGGCCTGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTggg                                        <  3:266673/148‑1 (MQ=255)
                                                                                                              tGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTAAATTggg                                        >  4:221962/1‑147 (MQ=255)
                                                                                                                  aTCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGAcg                                  >  2:217418/1‑149 (MQ=255)
                                                                                                                   tCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTAt                                                                                 <  4:169586/101‑1 (MQ=255)
                                                                                                                     aCGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGAcgtt                                <  5:280343/148‑1 (MQ=255)
                                                                                                                       gCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGAcgttcgt                             <  7:99121/149‑1 (MQ=255)
                                                                                                                           ggCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCtgt                                                                                     >  4:224799/1‑89 (MQ=255)
                                                                                                                           ggCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCtgt                                                                                     <  3:224799/89‑1 (MQ=255)
                                                                                                                            gCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGt                         >  1:256853/1‑148 (MQ=255)
                                                                                                                            gCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTg                        <  2:19615/149‑1 (MQ=255)
                                                                                                                             cTTCCGGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGc                       <  2:141570/149‑1 (MQ=255)
                                                                                                                                ccAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTAttt                                                  <  2:38111/119‑1 (MQ=255)
                                                                                                                                ccAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTAttt                                                  >  1:38111/1‑119 (MQ=255)
                                                                                                                                 cAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTAGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAAt                   <  2:178818/149‑1 (MQ=255)
                                                                                                                                  aGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATg                  >  3:193570/1‑149 (MQ=255)
                                                                                                                                         ggCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAAt             <  5:281326/147‑1 (MQ=255)
                                                                                                                                          gCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAATTCt          <  4:186885/149‑1 (MQ=255)
                                                                                                                                            aagagTCAAGGTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAATTc           >  6:143136/2‑146 (MQ=255)
                                                                                                                                            aagagTCAAGGTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAATTCTa         <  5:143136/147‑1 (MQ=255)
                                                                                                                                                  cACCTTCACTCTTGGTAGATACGCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGACGCCAATTTATCAACTGCCATGAGTATTTGGCAATTGGGCAGACGCTCGTTAGTGCAAATGGAAATTCTAGATTTcc  <  5:271288/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
TGTCAGAGCTTTTGCACCTTCTGGACGATCTTCAAGAGCGAGCTTGCCCGATACCACATCCACAAATTCACCAACGACATTCCAGTCGTTCGCTTGGGCCGCACGTTGGATGTAATCACGCTGGGCTTCCAGACCTAGGCCAGAGTCACCTTGACTCTTGGTAGATACTCGAATGTAAGCAACAACGTTTGTCATGATGATGGCTCGTCTGTGTATGAGGCCAATTTATCAACTGCCATGAGTATTTGTCAATTGGGCAGACGTTCGTTAGTGCAAATGGAAATTCTAGATTTCC  >  NC_002947/1277175‑1277469

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: ‑