Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,573,5000AG51.0% 57.0 / 77.6 51pseudogene (1087/1503 nt)yjiTpseudogene
Reads supporting (aligned to +/- strand):  ref base A (4/21);  new base G (26/0);  total (30/21)
Fisher's exact test for biased strand distribution p-value = 1.11e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.67e-09

AGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCGGG  >  NC_000913/4573355‑4573650
                                                                                                                                                  |                                                                                                                                                                
aGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTGGGGGGGGGAtt                                                                                                                                                            >  1:364744/1‑151 (MQ=255)
 gATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGAttg                                                                                                                                                           <  2:356643/151‑1 (MQ=255)
           aaGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGGTGGTTTTTtgggggat                                                                                                                                               >  1:151110/1‑146 (MQ=255)
               ctctGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGTGATTGTTGGGGGCAtt                                                                                                                                             >  1:175725/1‑148 (MQ=255)
                    gCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGGGGGGTGGTTGTTGGGGGGATTAAAAtt                                                                                                                                       >  1:165068/1‑149 (MQ=255)
                         gggCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACa                                                                                                                                <  2:493252/151‑1 (MQ=255)
                              aGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGGTGATTGTTGGGGGGATTAAACTTGATGAAAggg                                                                                                                            >  1:691050/1‑147 (MQ=255)
                              aGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTGGGGGGGTGATTTTTGGGGGCATTAAAAtt                                                                                                                                       >  1:239546/1‑139 (MQ=255)
                                     gCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCATGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGcc                                                                                                                <  2:599754/150‑1 (MQ=255)
                                           ctGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGGGGGTTGTTGGGGGGATTAAAATTGATGACAGTGAAATTGGCATTGGTg                                                                                                        >  1:145273/1‑151 (MQ=255)
                                             ggAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGt                                                                                                          <  2:343677/148‑1 (MQ=255)
                                               aaaaCAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGGAGATTTTTGGGGGGATTTAAATTTGTTGCAGTGGAAATTGCATTTggggggg                                                                                                      >  2:74719/1‑146 (MQ=255)
                                                aaaCAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGACTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAgg                                                                                                     <  2:37042/149‑1 (MQ=255)
                                                    agacagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCCGGGTGGGGGGGGGGTTTTTGGGGGGATTAAAATTGTTGGCAGGGGAAATGGCCTTTgggggggg                                                                                                     >  2:6226/1‑141 (MQ=255)
                                                      acagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGGGGGGGGATTGTTGGGGGGATTTAAATTTATGACAGTGGAAATTTCCTTTGGGAGGGGCCGtt                                                                                              >  1:553682/1‑150 (MQ=255)
                                                      acagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCCGGGTGGGGGGGGGATTTTTGGGGGGATTAAAATTTTTGACAAGGAAAATGGCATTTGGGAgggggcggt                                                                                              >  2:691385/1‑143 (MQ=255)
                                                        agGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGAGGGGTGATTGTTGGGGGGATTAAAATTGATGACAGGGAAAATGCCATTGGTgggggggcggt                                                                                              >  1:247499/1‑141 (MQ=255)
                                                        agGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTGGGGGGGAGATTTTTTGGGGGATTTAAACTTGTTGAAGGGAAATTTGCCTTTgggggggggcggt                                                                                                >  2:743209/1‑137 (MQ=255)
                                                            aaCAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGTGGTTTTTTGGGGCATTAAAATTTTTGACAGTGAAATTTCCCTTGGGGGGGGGCCGTTTACCtt                                                                                        >  1:418995/1‑150 (MQ=255)
                                                                   cGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGCGGGGGGGTGGTTGTTTGGGGCATTAAACTTTCTGGCAGTGAAAATGGCCTTTGGGGGGGGGCGTTTAACTTTctcctt                                                                                  >  1:392994/1‑145 (MQ=255)
                                                                   cGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTg                                                                                <  1:134986/151‑1 (MQ=255)
                                                                    gATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTTGGGGGGAGATTGTTGGGGGGATTATAATTGTTGGAACTGAAAATGTCCTTGGGGGGGGGGCGTTAAACTTccttctt                                                                                 >  2:552689/1‑143 (MQ=255)
                                                                    gATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGTGATTGTTGGGGGGATTAAACTTGATGACAGGGAAATTGCCCTTGGGGAGGGGGCGTTTAACTTCAttgttg                                                                                >  1:283532/1‑150 (MQ=255)
                                                                       tACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATg                                                                             <  1:113736/150‑1 (MQ=255)
                                                                        aCGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCa                                                                           <  1:229372/151‑1 (MQ=255)
                                                                        aCGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTGGGGGGGTGATTGTTGGGGGGATTAAAATTTGTTACAGTGAAAATGTCCTTTGGGGGGGGCCGTTTACCCTCCTCGtttgt                                                                              >  1:239988/1‑145 (MQ=255)
                                                                         cGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGAGAAATATTGGGGGGATTAAAAATTATGAACATGAAATTTGCATTGGGGGGGGGGCGGTAACCTTTATAGTTGAt                                                                              >  2:200560/1‑147 (MQ=255)
                                                                              aaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGCTGGGGGGGGATTTTTGGGGGGCTTAAAACTTTTGGAAGGGGAAATTGCATTGGTGGGGTGGCGTTTAACTTCCTCGTTTATGCAggt                                                                        >  2:415518/1‑146 (MQ=255)
                                                                              aaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGTGGTTGTTTGGGGGATTTAAATTTGTGACAGTGAAAATTCCCTTGGTGGGGGGGCCGTTACCTTCATCGTTTATGCa                                                                           >  1:253438/1‑145 (MQ=255)
                                                                                gCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGGGGGGTGGTTGTTTGGAGCATTAAAACTTATGACAGTGGAAATGCCCTTGGGGGGGGGCCGTTAACCCTTATCGTTGGTGGAGAACaa                                                                     >  1:583535/1‑149 (MQ=255)
                                                                                gCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATg                                                                   <  2:24388/151‑1 (MQ=255)
                                                                                  gAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGGGGGGTGGTTGTTTGGAGCATTAAAATTTATGACAGTGGAATTTCCATTTGTGGGGGGCCGTTTAACTTCATCGTTGATGCAGATCAATgg                                                                  >  1:292303/1‑150 (MQ=255)
                                                                                       gagaTTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGtt                                                             <  2:648181/150‑1 (MQ=255)
                                                                                            ttGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGTGGGGGGGTGATTGTTTGGGGGCTTTAAATTTATGAAAGGGGAAATTGCCTTTGGGGGGGGGCGGTTAACTTTATCTTTTATGGAGATCAATTGCTGTTTCAggg                                                       >  1:608648/1‑151 (MQ=255)
                                                                                              ggcaggcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGAc                                                     <  1:66107/151‑1 (MQ=255)
                                                                                                 aggcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGTGGGGGGGTGATTTTTGGGGGGATTTAAATTTATGAAAGGGGAAATGCCCTTGGGGAGGGGCCGTTAAACTTCATCGTTGATGGAGATCAATGGGTGTTTCAGGGGCAgg                                                  >  1:651173/1‑151 (MQ=255)
                                                                                                    caAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGctt                                               <  1:6226/151‑1 (MQ=255)
                                                                                                    caAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGct                                                <  1:46211/150‑1 (MQ=255)
                                                                                                     aaaaTCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCGGGGGGGGGGGTTTTTGGGGGCATTTAAATTTTTGACAGTGAAAATGTCCTTTGTGGGGGGGCCGTTACCTTTCTTGTTTATGCCGATAAAAAGCTGTTTTAGGGGCAGGctt                                               >  2:466306/1‑150 (MQ=255)
                                                                                                     aaaaTCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGTGATTGTTGGGGGCATTAAACTTGATGACAGTGAAAATTCCATTGGGGAGGGGCCGGTAAACTTCATCGTTGTTGCAGAGAAAAGGCTGTTTAAGGGACAGGctt                                               >  1:228554/1‑150 (MQ=255)
                                                                                                                  aGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGa                                 <  1:440609/151‑1 (MQ=255)
                                                                                                                       tGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagca                             <  1:693033/150‑1 (MQ=255)
                                                                                                                        gTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagcagc                           <  1:346905/151‑1 (MQ=255)
                                                                                                                        gTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagcagc                           <  1:291005/151‑1 (MQ=255)
                                                                                                                        gTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagcag                            <  2:591745/150‑1 (MQ=255)
                                                                                                                               gTGGCTCGTGCTGGAGGGATGATTGTTGGGGGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGGGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGtt                     >  2:730496/1‑150 (MQ=255)
                                                                                                                                   cTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGAt                >  1:264030/1‑151 (MQ=255)
                                                                                                                                     cGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATtg              <  2:36630/151‑1 (MQ=255)
                                                                                                                                      gTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATtgt             >  1:498111/1‑151 (MQ=255)
                                                                                                                                            ggAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTcc        <  1:658277/151‑1 (MQ=255)
                                                                                                                                                ggATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCg    <  1:246087/151‑1 (MQ=255)
                                                                                                                                                  atgatTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCggg  >  1:150197/1‑151 (MQ=255)
                                                                                                                                                  |                                                                                                                                                                
AGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCGGG  >  NC_000913/4573355‑4573650

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: