Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,406,760 C→A 8.0% G362C (GGC→TGC)  PP_3889 ← putative Phage integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,406,7600CA 8.0% 146.7 / 3.1 50G362C (GGC→TGC) PP_3889putative Phage integrase
Reads supporting (aligned to +/- strand):  ref base C (23/23);  new base A (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

GATTTCTGCGGGATTTCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGTCTCACTCAGG  >  NC_002947/4406615‑4406908
                                                                                                                                                 |                                                                                                                                                    
gATTTCTGCGGGATTTCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAg                                                                                                                                                   >  3:321391/1‑149 (MQ=255)
      tGCGGGATTTCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGtgtg                                                                                                                                             >  6:332020/1‑149 (MQ=255)
             tttCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTcagc                                                                                                                                      <  4:328761/149‑1 (MQ=255)
             tttCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTcag                                                                                                                                       >  3:133850/1‑148 (MQ=255)
              ttCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTcag                                                                                                                                       >  1:299889/1‑147 (MQ=255)
               tCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCACAGCGTGTGGTTcagc                                                                                                                                      <  6:201751/147‑1 (MQ=255)
               tCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCACAGCGTGTGGTTcagc                                                                                                                                      >  3:207052/1‑147 (MQ=255)
               tCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCACAGCGTGTGGTTcagc                                                                                                                                      >  5:201751/1‑147 (MQ=255)
               tCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCACAGCGTGTGGTTcagc                                                                                                                                      <  4:207052/147‑1 (MQ=255)
                 aaaTAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGc                                                                                                                                                  <  3:62133/133‑1 (MQ=255)
                 aaaTAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGc                                                                                                                                                  >  4:62133/1‑133 (MQ=255)
                                aaGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTgg                                                                                                                    <  4:133850/148‑1 (MQ=255)
                                  ggCCGTGGATGGCTACGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGtt                                                                                                                                          <  5:285538/124‑1 (MQ=255)
                                  ggCCGTGGATGGCTACGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGtt                                                                                                                                          >  6:285538/1‑124 (MQ=255)
                                           tGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGcc                                                                                                         >  1:340932/1‑148 (MQ=255)
                                             gCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAg                                                                                                      >  5:232931/1‑149 (MQ=255)
                                             gCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCACCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAg                                                                                                      <  1:241699/149‑1 (MQ=255)
                                              cTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATCTAGGTGCTGGCCATCTTGACCATCCTGTGGTTCAGCAGCATCTCGACGATCTGGCCGTCGATGCCGAgg                                                                                                     >  2:191301/1‑149 (MQ=255)
                                               tGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGgt                                                                                                    >  6:257786/1‑149 (MQ=255)
                                               tGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATAGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGgt                                                                                                    >  1:103966/1‑149 (MQ=255)
                                                  gAAGCCGATCCGATCAAGCCAGGTGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGgtccg                                                                                                 >  7:242246/1‑149 (MQ=255)
                                                            cgatcAAGCCAGGCGTGCCACTTCTGGATCGCCAAGTTGCGCTGGTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCATCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGtgc                                                                                        <  1:191301/148‑1 (MQ=255)
                                                            cgatcAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGtgct                                                                                       <  5:332020/149‑1 (MQ=255)
                                                                 aaGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCgg                                                                                   <  2:299889/148‑1 (MQ=255)
                                                                  aGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGa                                                                                 <  4:321391/149‑1 (MQ=255)
                                                                    ccAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGaca                                                                               >  3:63875/1‑149 (MQ=255)
                                                                                      cAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGc                                                             <  5:257786/149‑1 (MQ=255)
                                                                                                  gcgcTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCg                                                  <  2:103966/148‑1 (MQ=255)
                                                                                                        ctCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGc                                            <  2:340932/148‑1 (MQ=255)
                                                                                                         tCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCACCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGccc                                          >  1:195207/1‑149 (MQ=255)
                                                                                                          ccATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGccc                                          >  8:113040/1‑148 (MQ=255)
                                                                                                           cATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTgg                                                              <  5:330534/127‑1 (MQ=255)
                                                                                                           cATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTgg                                                              >  6:330534/1‑127 (MQ=255)
                                                                                                                ccTGGGTGTGGATGTAGGTGCTGGCGTTCTTGCCCATCGTGTGGTTCAGCATCATCTCGCCGATGTGGCCGTCGATGCGGAGGTCCGTCCATGTGCTGCGGGACACCTTTCGCAGTTCGTTGCTTGTCCACTCGCCCTGCCCCAGCCgg                                   <  7:136178/149‑1 (MQ=255)
                                                                                                                 cTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCggg                                  >  8:85978/1‑149 (MQ=255)
                                                                                                                    ggTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTg                                >  6:257500/1‑148 (MQ=255)
                                                                                                                          gATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCa                         >  7:178987/1‑149 (MQ=255)
                                                                                                                            tGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATg                       <  8:178987/149‑1 (MQ=255)
                                                                                                                             gTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGt                                 <  3:68217/138‑1 (MQ=255)
                                                                                                                             gTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGt                                 >  4:68217/1‑138 (MQ=255)
                                                                                                                                  tGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGc                  <  4:180351/148‑1 (MQ=255)
                                                                                                                                  tGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGc                  >  3:180351/1‑148 (MQ=255)
                                                                                                                                       gCGATCTTGCCCAGCGTGTGGTTCAGCAGCATTTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGt            >  1:302701/1‑149 (MQ=255)
                                                                                                                                       gCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTgg              <  7:113040/147‑1 (MQ=255)
                                                                                                                                       gCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGt            <  6:232931/149‑1 (MQ=255)
                                                                                                                                       gCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGt            <  2:343000/149‑1 (MQ=255)
                                                                                                                                       gCGATCTTGCCCAGCGTGTGGTTCACCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGt            <  2:195207/149‑1 (MQ=255)
                                                                                                                                         gATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGtct          >  3:108797/1‑149 (MQ=255)
                                                                                                                                            cTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCGGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGTctca        <  4:63875/148‑1 (MQ=255)
                                                                                                                                               gCCCAGCGTGTGGTTCAGCAGCATTTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGtct          <  2:302701/143‑1 (MQ=255)
                                                                                                                                                cccAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCGGGGTCTCACTCAg   >  4:189353/1‑149 (MQ=255)
                                                                                                                                                 ccAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGTCTCACTCAgg  >  8:290196/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
GATTTCTGCGGGATTTCAAATAAGGCCTCTTTAAGGCCGTGGATGGCTGCGAAGCCGATCCGATCAAGCCAGGCGTGCCACTTCTCCAGCGCCAACTTGCGCTGCTCCATGGCCTGGGTGTGGATGTAGGTGCTGGCGATCTTGCCCAGCGTGTGGTTCAGCAGCATCTCGCCGATGTGGCCGTCGATGCCGAGGTCCGTCCAGGTGCTGCGGGACACCTTGCGCAGGTCGTGGCTGGTCCACTCGCCCTGCCCCAGCCGGGTGAACACCATGCTCGCCTGGGTCTCACTCAGG  >  NC_002947/4406615‑4406908

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: ‑