Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,573,4960AG51.0% 32.0 / 75.8 50pseudogene (1083/1503 nt)yjiTpseudogene
Reads supporting (aligned to +/- strand):  ref base A (4/20);  new base G (25/0);  total (30/20)
Fisher's exact test for biased strand distribution p-value = 3.76e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.16e-09

CATTTGTGAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCC  >  NC_000913/4573346‑4573644
                                                                                                                                                       |                                                                                                                                                              
cATTTGTGAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGa                                                                                                                                                                <  1:281450/151‑1 (MQ=255)
         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                     <  1:291005/151‑1 (MQ=255)
                                                                                                                                 gTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagcagc                     <  1:346905/151‑1 (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)
                                                                                                                                                       |                                                                                                                                                              
CATTTGTGAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTGAAATTGCCATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCC  >  NC_000913/4573346‑4573644

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: