Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913266,3490CA56.0% 30.4 / 84.4 50V69F (GTT→TTT) yafYlipoprotein, inner membrane; degP regulator; CP4‑6 prophage
Reads supporting (aligned to +/- strand):  ref base C (4/18);  new base A (27/1);  total (31/19)
Fisher's exact test for biased strand distribution p-value = 6.79e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.82e-05

CACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGAT  >  NC_000913/266209‑266499
                                                                                                                                            |                                                                                                                                                       
cACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAgggg                                                                                                                                               >  2:871899/1‑149 (MQ=255)
  cctcctGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTggg                                                                                                                                             <  2:587143/151‑1 (MQ=255)
  cctcctGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTgg                                                                                                                                              <  2:118430/150‑1 (MQ=255)
   ctcctGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGTAGTAAAAACTGCCAgggggg                                                                                                                                             >  1:738153/1‑150 (MQ=255)
        ggTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGa                                                                                                                                       <  1:898716/151‑1 (MQ=255)
        ggTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTAAGTAAAAACTGCCAGGGGGGGCCgg                                                                                                                                        >  1:282930/1‑150 (MQ=255)
           aTTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAAGTAAAAACCGCAAGGGGGGGCCgggaa                                                                                                                                     >  2:661445/1‑147 (MQ=255)
             tCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAAGTAAAAACCGCAAGGGGGGGCCGGGTaa                                                                                                                                    >  1:60002/1‑149 (MQ=255)
               cAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAACCGCAAGGGGGGGCCgggaaa                                                                                                                                    >  1:642272/1‑143 (MQ=255)
                       tGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAGGGGGGGCCGGATAAGTAGTCAAcc                                                                                                                         >  1:765942/1‑149 (MQ=255)
                        gTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCtgt                                                                                                                      <  2:901701/151‑1 (MQ=255)
                           aTCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAACCCGTAAGGGGGGGCCCCAGAAAGAGTCAACCagt                                                                                                                      >  1:640080/1‑148 (MQ=255)
                                cAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTAAGTAAAAACTGCAAGGTGGGACCGGATAAATAGTCAAACCGTGACCAtt                                                                                                               >  1:709216/1‑150 (MQ=255)
                                 aaTACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAACCGCAAGGGGGGGGCGGGGAAATAGGCAAACTTTGACCCtt                                                                                                               >  1:277404/1‑149 (MQ=255)
                                  aTACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAAGGAAAAACCGCAAAGGGGGGCCGGGAAAAAAGTCAAACTGTGAACcttctt                                                                                                            >  1:497391/1‑151 (MQ=255)
                                    acacAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAAGGGGGGCCGGATAAAAGGGCAACCCGTGAGCcttctt                                                                                                            >  2:952383/1‑149 (MQ=255)
                                      acaGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACCTAAAAACTGCAAAGGGGGACCGGGTAAGGAGTCAACCTGTGACCAttctt                                                                                                            >  1:941243/1‑147 (MQ=255)
                                       caGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTg                                                                                                       <  2:427958/151‑1 (MQ=255)
                                        aGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGa                                                                                                      <  2:228675/151‑1 (MQ=255)
                                        aGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAACCACCAAGTGGGGCCGGGAAAGGAGTCAAACTCTGACCCttcttctccg                                                                                                       >  1:503464/1‑146 (MQ=255)
                                           gcATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGAcat                                                                                                   <  2:228902/151‑1 (MQ=255)
                                                catcaGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAAGGGGGGCCGGGTAAAGAAGCAACCTGTGACCATTCTTTCCCGACATCATcc                                                                                              >  1:895246/1‑151 (MQ=255)
                                                catcaGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAACTTCAAAGTGGGACCCGCTAAGGAGTGAAACTCGGACCCCTCTTCGCTgccggca                                                                                                 >  1:800777/1‑142 (MQ=255)
                                                      tGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAAACCGCAAGGGGGGGCCGGATAAGTAGGCAACCCGTGGCCAATCTTCGCTGACATCATCCttgtgg                                                                                        >  2:214949/1‑151 (MQ=255)
                                                      tGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCCAGGGGGGGCCGGGGAAATAGTCAACCCGTGACCCTTCTTCGCCGACATCATCCtggtgg                                                                                        >  2:82366/1‑151 (MQ=255)
                                                                      tCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAACCTGCCAGGGGGGACCGGGGAAATAGGCAAACTGTGACCCTTCTTCGCTGACATCCTCCTCGTGGCTGGCCACAt                                                                              >  1:869434/1‑145 (MQ=255)
                                                                         tGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTATAAACTACAAAGGGGGGCCGGGAAAGAAGTCAACCTGTGAACATTCTTTGCTGACATCATCCTGGTGGGTGGCCACAACAATGaaa                                                                      >  2:668636/1‑150 (MQ=255)
                                                                          gCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGGAAAAACCGCAAAGGGGGAGCGGGGAAAGAGTCAACCCGTGACCATTCTTCGCTGGCAAAATCCCGGTGGGGGACCACATCACCGaaa                                                                      >  2:103998/1‑149 (MQ=255)
                                                                            atatCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAAcgcg                                                                  <  2:642082/151‑1 (MQ=255)
                                                                             tatCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACCGCAAGGTGGGGCCGGGGAAGTAGTCAACCCTGTACCCTTTTTCGCCTACACCCTCCTGGTGGCCGACCACCACACCTAAACGCgg                                                                 >  1:80526/1‑151 (MQ=255)
                                                                              atCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCgg                                                                 <  1:952180/150‑1 (MQ=255)
                                                                              atCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGt                                                                <  2:632281/151‑1 (MQ=255)
                                                                                ccACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAACCTGCAAAGGGGGACCCGATAAGTAGTCAAACCGTGACCATTCTTCGCCGACATCATCCCGGTGGCTGACCACATCACTGAAACGCGgggg                                                              >  1:186327/1‑151 (MQ=255)
                                                                                 cACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTggg                                                             <  1:845811/151‑1 (MQ=255)
                                                                                  aCGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAGGGGGGACCGGGTAAGTAGTCAACCTGTGAGCATTCTTTGCTGACATCATCCTGGTGGGTGGCCACCTCACTGAAACGCGgggggg                                                            >  1:620145/1‑151 (MQ=255)
                                                                                      ggTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGa                                                         <  2:582264/150‑1 (MQ=255)
                                                                                         agtagtaACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAAGTAAAAACTGCCAGGGGGGGCCGGATAAGTAGGCAACCTGTGACCATTCTTTGCTGACATCATCCTGGGGGGTGACCACATCACTGAAAACCGggggggggggg                                                       >  1:65818/1‑144 (MQ=255)
                                                                                           tagtaACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCCGCCAGGGGGGGCCGGATAAGAAGGCAACCCGTGACCCTTCTTCGCTGACATCATCCTGGGGGCTGACCACATCACTGAAACGCGggggggggggggcc                                                    >  1:115992/1‑142 (MQ=255)
                                                                                               aaCTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGCAAAAACCGCAAGGAGGGGCCGGAAAAGGAGGCAAACCGTGGCCCTTCTTTGCCGACCTCAACCCCGTGGCTGGGCCCATCACTGAAAAGCGggggggggggggccct                                                  >  2:373045/1‑138 (MQ=255)
                                                                                                   gCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAAtt                                             <  1:93895/149‑1 (MQ=255)
                                                                                                      aTCCTCGCAGCCATCGGGCGACTGGCGGGTATGTAAAAACTGCGAGGGGGGGGCGGATAAATAGGCAAACCGTGGCCCTTCTTCTCCGTCATCATCCCGGGGGCTTCCCACAACACCGGAACCGGGGGGGGGGGGGGCCTTtaa                                               >  1:14270/1‑144 (MQ=255)
                                                                                                         cccgcgGCCATCGGGCGCCTGGCCGGTACGTAAAGACTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACGATTCTTCGCGGACATCATCCTGATGTCTGCCCACAGCACTGAAGCGGGGTGGGGTGTCGTCCTTATAtttc                                           <  2:937917/143‑2 (MQ=255)
                                                                                                         cTCGCAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAAGTGGGGCCGGATAAATAAGCAAACTGTGACCATTCTTCGCTGACATCATCCTGGGGGCTGGCCACACCACTGAAAAGCGGTGGGGGGAGGGCCTTAAATTTTCTg                                        >  2:452678/1‑148 (MQ=18)
                                                                                                           cGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGc                                   <  2:59989/151‑1 (MQ=255)
                                                                                                             cAGCCATCGGGCGACTGGCGGGGACGTAAAAACTGCAAGGGGGGGCCGGAGAAATAGTCAACCTGTGACCCTTCTTCGCTGACATCATCCTGGTGGCGGAACCCATCACTGAAACGCGGGGGGGGGGGGGCCTTAAAATTACTGAttggc                                  >  2:343919/1‑146 (MQ=18)
                                                                                                                ccATCGGGCGACTGGCGGGTACGTAAAAACTGCAAGGGGGGGCCGGGTAAGTAGTCAACCTGTGACCATTTTTCGCTGACATCATCCTGGGGGGTGACCACATCACTGAAACGCGGGGGGGGGGGGGCCTTTAATTTACTGATGGCCtt                                >  1:325227/1‑149 (MQ=255)
                                                                                                                  aTCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAgg                            <  1:587088/151‑1 (MQ=255)
                                                                                                                       gCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGtcatc                       <  2:577647/151‑1 (MQ=255)
                                                                                                                                 ggTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCa             <  2:123408/151‑1 (MQ=255)
                                                                                                                                     cGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGc         <  2:277332/151‑1 (MQ=255)
                                                                                                                                            ccTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGAt  >  1:541324/1‑151 (MQ=255)
                                                                                                                                            |                                                                                                                                                       
CACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGTAAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTGACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGAT  >  NC_000913/266209‑266499

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: