Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,996 G→T 20.3% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,560,9960GT20.3% 86.1 / 3.3 53intergenic (+98/‑372)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (20/21);  new base T (7/5);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 7.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAA  >  NC_000913/2560853‑2561134
                                                                                                                                               |                                                                                                                                          
gttcAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                                                      <  2:541631/147‑1 (MQ=255)
  gCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTACATGAATTCAGGTGGGTCAAAAGTTGCCGTTTGTGGAGGGTAATATTTTGAAGTTAAGGTg                                                                                                                                    >  1:766307/1‑150 (MQ=255)
    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGTTAAggagtg                                                                                                                                  >  1:981410/1‑146 (MQ=255)
    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGTTGGGTCAAATGTTGCATTTAAGGAggg                                                                                                                                  >  2:1174747/1‑150 (MQ=255)
    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTGCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGACAAAAGTTGCCGTTAAGGTggg                                                                                                                                  <  1:820202/150‑1 (MQ=255)
            ccAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTTGGTCAAAAGTTGACTTTAAGGATGCTCAAAAGt                                                                                                                          >  2:399783/1‑150 (MQ=255)
              aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTg                                                                                                                        >  1:907429/1‑150 (MQ=255)
               gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGc                                                                                                                       <  2:520506/150‑1 (MQ=255)
                 tattatTCAAGCAGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTCCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCg                                                                                                                     <  2:1125410/150‑1 (MQ=255)
                   ttattCAACCAGTAAAAGATGAAATTAAGTTATCAGTAGTGCAATGTTAACGCCATTTCTTTTCCTTAATTACATGAATTCAGGTGGGTAAATTTTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGtt                                                                                                                   <  2:1546816/150‑1 (MQ=16)
                        cAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTAAAAAGTTGCCGTTAAGGAGGGTCAAAATTTTCCTTTAACGt                                                                                                              >  2:1119789/1‑150 (MQ=255)
                         aaGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                             <  1:909090/150‑1 (MQ=255)
                         aaGCCGTACAACAAGAAATAACGGAATCAGGCGGGCAATGTTCCCGCATTTTCTTTGCCTTAAATCCATGAATTCAGGTGGGGCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                             <  2:871968/150‑1 (MQ=255)
                         aaGCCGTACAAAATGAAATAACGGAATCTGTCGGGCAATGTTCGCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGTTGGGTCAAAAGTTGCCGTTAGTGGGGGGTGAAAAGTTGCCGTTAAGGTGGGGCTAAAGTTGCCGTTAAGTTg                                                                                                             <  2:1326529/150‑1 (MQ=255)
                          aGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                            >  1:573806/1‑150 (MQ=255)
                             cGTACAACATTAAATAAATTAATAAGTTGGGCATTTATCCAGCCTTTTGTTTTCCTTAAATTAATGAATTCATGTGTGTCAAAATTTGCCTTTATTGTTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTc                                                                                                         <  2:1107157/150‑1 (MQ=16)
                                          ttAACTGAATCAGTCGGGCAATGTTCCCGCGTTTTCTTTGCCATAATTCAATGAATTCTGGTGTGTCAAAAGTTTCCCTTATTGGTGGGTCAAATGTTGCCTTTAAGGTTGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAg                                                                                            <  1:578008/149‑1 (MQ=37)
                                                    cAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGGGTCAAAATTTGACTTTAAGGAGTGTCTATATTTCCGGGTAAGGTGAGTAAAAAATTGACTAGTAAGAATTct                                                                                  >  1:20130/1‑150 (MQ=255)
                                                     cgccGGGCATTGATCCCGCCATTGCTTTTCCTTAAATCCATGAATTCCGGTGGGTAAAAAGTAGCCCTTATTGGTGGGTCAAAACTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTcta                                                                                 <  1:658758/147‑1 (MQ=25)
                                                          ggCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGTCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGACGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTctaaaatt                                                                            >  2:1709699/1‑145 (MQ=255)
                                                             aaTGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCTAAAGTTGCCGAGTAAGAATTCTAATATTatt                                                                         >  1:1203429/1‑148 (MQ=255)
                                                                     cggcctttCTTTGCCATAAATCCCTGTATTCAGGCGGGTCAAAAGTTGCCGTTACTGGGGGGGCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAg                                                                 <  1:370196/145‑1 (MQ=37)
                                                                     cGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGATGGGTAAAATTTTGACTTTAAGGAGGGTCAAAATTTGACGTGAAGGTTTCTGAAAATTTGAATAGTAAAAATTATAATATTAAAAAtaatac                                                                 >  2:1128773/1‑145 (MQ=255)
                                                                      gCCTTTTCTTTGCCTTAATTCCATGAATTCAGGGGGGTCAAAACTTGCCGTTATTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAgg                                                                <  1:1324279/150‑1 (MQ=255)
                                                                          tttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGGTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGACGAGTAAGAATTCGACTATTAAGAATTCTAGGCGAc                                                            >  1:1584207/1‑150 (MQ=255)
                                                                                   cTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCCTAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGTAGtttt                                                   >  2:378706/1‑150 (MQ=255)
                                                                                       ataccATCAATTCAGCTGCGTCAAAAGCACCCTTTCGTGGGGCGTCAAACGGTGCCGTTACGGTGGGTCAAAAGTTGCCCTTAAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               <  1:1684440/147‑1 (MQ=255)
                                                                                       aatccatccaTTCAGGGTGGTCCACAGTGGCCGTTAGGGGTGGGTCAAAAGCTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               <  1:879234/148‑1 (MQ=25)
                                                                                       aTTCCATGAATTCAGGTGGGTAAATATCAGGCTTTATTTGTGGGTAAAAAGATGCCTTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               <  1:1119789/150‑1 (MQ=25)
                                                                                         tCCATGAATTCAGGTTGGTAAAAATATGGCCTTATTGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGcc                                             <  2:573806/150‑1 (MQ=37)
                                                                                          ccATGAATTCAGTTGGGTAAAAAGTTGCCGTTAGTGGTGGGTCAAAACTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCt                                            <  1:478581/150‑1 (MQ=255)
                                                                                             tGAATTCCGGCGCGACAAAATTAGCCGTTAGTGGGGGGTCAAAAGCCGCCGTTAAGGTGGCTCAAAAGTAGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTccc                                         <  1:1372528/150‑1 (MQ=37)
                                                                                              gAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGGGTAAAAATTTGCCTTGTAGGAGGGTCAAAAGTTGCAGGGTAGGTGTGTGAAATTTTGCGGAGAAAGAAGTCTACAATTAGGAATTATAGGCGTCGTGATTTTTGTAgtgtaggg                                        >  2:959804/1‑143 (MQ=12)
                                                                                                     ggTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTGAAGGTGGCGCAAAATTTTCAGAGTAACAATTATACTATTAAGAATTCTAGGCGACGGGCGTTTTTTATCCTACcgctcgtta                                 >  2:1145528/1‑147 (MQ=21)
                                                                                                          gTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTTATGTGGGGCAAAAGTTTACGAGTAAGAATTCTACTATTAAGATTACTAGTCGACGGGAGTTATTAATACTCCAGCTCGGTCATaga                            >  1:1058462/1‑150 (MQ=21)
                                                                                                          gTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCACGGTCGGTCATaga                            >  1:1331478/1‑150 (MQ=255)
                                                                                                           tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGGTAAGGTGGGTCAAAAGTTTCCGTTAAGGTGGGGGAAATGTTGCGTAGTAAGCATTCTAATATTAAGAATACTATCCGTCTGGAGAGTTTTAGACGTCCGGTCGATCATagac                           >  2:1060994/1‑149 (MQ=255)
                                                                                                             aaaaGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagagag                         >  2:560326/1‑150 (MQ=255)
                                                                                                             aaaaGTTGCCGTTACTGGGGGGTCAAAACTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagagag                         <  1:755917/150‑1 (MQ=255)
                                                                                                             aaaaGTAGCCGTTTGTGGTGGGTCAAAAGTTGCCTTTAAGTTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagagag                         <  1:1345359/150‑1 (MQ=255)
                                                                                                             aaaaCTTGCCCTTAGTGGTGGGTCAAAACTCGCCGTTAAGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGGTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagagag                         <  1:582942/150‑1 (MQ=39)
                                                                                                                atatGCCTTTATTGGGGGGTAAAAAGTTGCCGTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCg                      <  2:313629/147‑1 (MQ=38)
                                                                                                                aGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTAGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCg                      >  1:1257861/1‑150 (MQ=255)
                                                                                                                   aggccttATTGGTGGGTCAAAAGTTGCCTTTAATGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCt                   <  2:1462525/145‑1 (MQ=38)
                                                                                                                     ccGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCGTag                 >  1:1280850/1‑150 (MQ=255)
                                                                                                                        ttAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATAAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTACCGGTCGGTCATAGAGAGTCGCCTAGAGt              >  2:766204/1‑150 (MQ=255)
                                                                                                                            gtgggggTAAAAAGGTGCCTTTAAGGTGGGTCAAAAGGTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa          <  1:555477/146‑1 (MQ=39)
                                                                                                                             ggtggGTCAAAAGTTGACGTTACTGCGGGTCAAACGTTGCTCTTAAGGTTGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCAGGTCGGTCATAGAGAGTCGACTAGAGTTAAAc         <  2:1617016/150‑1 (MQ=255)
                                                                                                                                  gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaat    >  1:1553000/1‑149 (MQ=255)
                                                                                                                                  gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaag    >  1:1394383/1‑150 (MQ=255)
                                                                                                                                  gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaag    >  1:1614973/1‑150 (MQ=255)
                                                                                                                                  gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaag    >  2:694090/1‑150 (MQ=255)
                                                                                                                                    cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTTAGAATTCTAGGCGACGGCTGTATTTTAGCCTCCCGGTCGGTCATAGAGAGTCGACTAGAGTTAATCAtaagaa  >  2:894425/1‑150 (MQ=37)
                                                                                                                                               |                                                                                                                                          
GTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAA  >  NC_000913/2560853‑2561134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑