Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,100,573 A→G 13.7% intergenic (‑48/‑237) rhaT ← / → sodA rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,100,5730AG13.7% 109.3 / 2.2 52intergenic (‑48/‑237)rhaT/sodArhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn)
Reads supporting (aligned to +/- strand):  ref base A (23/21);  new base G (2/6);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 2.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTTTTTACTTTTTTGAACGGAGCGTAAAAACAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCTTACGAAAAGTACG  >  NC_000913/4100432‑4100711
                                                                                                                                             |                                                                                                                                          
aTTTTTTTACTTTTTTGAACGGAGCGTAAAAACAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCCCATCTCCGACGAGATGAg                                                                                                                                           >  1:315638/1‑143 (MQ=255)
          ttttttGAACGGAGCGTAAAAACAGGCTGCACTGGCCGCGCCGATCAACTGCCAAAATATCCCCATCGTGATCGCGTTAGTCATCTTCTTATCCTCATCATTTGTCGTCGCGGCACATCTCCGAAGAGATgtgtgtcacagta                                                                                                                                 >  1:655134/1‑136 (MQ=255)
          tttcttGAACGGAGCGTAAAAACAGGCTGCACTGGCCTCGCAGTTCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTGATCCTTTTTCGTCGCGTCGCATCGTCGCCCAGTTGAGTGTtaaactt                                                                                                                                 >  2:823420/1‑140 (MQ=255)
              ttGAACGGAGCGTAAAAACAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGCTGAGGGTAAAAATCGTGc                                                                                                                             >  1:89429/1‑143 (MQ=255)
                    ggAGCGTAAAATCAGTCTGCACGGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGa                                                                                                                       <  2:911986/143‑1 (MQ=255)
                         gTAAAACCGGGCTGCACTCGCCGCGCCGATCAAATGCCAACATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAAc                                                                                                                  <  1:782245/143‑1 (MQ=255)
                           aaaaaCAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAACGTCGTGCTGTCGATTaaacc                                                                                                                >  2:651719/1‑140 (MQ=255)
                            aaagCAGGCTCCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCACCTTCTTATCCTCAGCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCtt                                                                                                               <  2:7493/143‑1 (MQ=255)
                             aaaCAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATACTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCCAGCCGTCGATTAAGCttt                                                                                                              >  2:754253/1‑143 (MQ=255)
                              aaCAGGCTACACTGGCCGCGCCGATGAAATGCCAAAATACCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTc                                                                                                             <  1:710688/143‑1 (MQ=255)
                                  ggCTGCACTGGCCGCGCCGGTCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCt                                                                                                         <  2:642106/143‑1 (MQ=255)
                                  gccTGCATTGGCCTGGCCGATCAAATGCCAAAATATCCCCAGTGTAATCGCGTTACTCAGCTTCGTATCCTCATCATTTTTCGTCGCGTCACACCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCt                                                                                                         <  2:424103/141‑1 (MQ=255)
                                     ttgaCTGGCCGCGCCGATCATCTGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCTTTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGtt                                                                                                      <  2:409364/140‑1 (MQ=255)
                                     tGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATGGTGCTGTCGATTAACCTTTCGCCTGtt                                                                                                      >  2:494985/1‑143 (MQ=255)
                                            gCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATCAAGCTTTCGCCTGTTGccgccg                                                                                               >  2:128259/1‑143 (MQ=255)
                                             ccGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCCCGTCACATCTCCGTCGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGt                                                                                              <  1:285627/143‑1 (MQ=255)
                                              cgcgCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGtt                                                                                             >  1:545715/1‑143 (MQ=255)
                                                  ccGCTCAAATGCCAAAATATCCCCATCCGAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCGCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCg                                                                                         <  1:910775/143‑1 (MQ=255)
                                                    gATCCAATGCCCAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGAt                                                                                       <  2:937055/143‑1 (MQ=255)
                                                        aaaTGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTAc                                                                                   <  2:740735/143‑1 (MQ=255)
                                                              cAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCaa                                                                             >  2:88028/1‑143 (MQ=255)
                                                              cAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCaa                                                                             >  2:88006/1‑143 (MQ=255)
                                                                aaaTATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGCTGAGTGTAAAACTCGTGCTGTCGATTAACCTTTCGCCCGTTGCCGCCGTTGTCGATTTACTgaggatc                                                                           >  1:287018/1‑137 (MQ=255)
                                                                   tatCCCCCGCGGAAACGCGTTACTCCCCTCCTTACCCGCGTCATGTTTCGTCGCGTCACATCTCCGACGGGATCGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACg                                                                        <  2:410580/143‑1 (MQ=255)
                                                                   tatCCCCATCGTAATCGCGTTACTCATCTTCTTACGCTAACAGACCTAAGTGGGGTCATGCATCCTGCGCGGTGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACg                                                                        <  2:415640/143‑1 (MQ=255)
                                                                        ccATCGTAATCGCGTTACTCATCTTGTTATCCTCATCATTTTTCGTCGCGTCACATCCCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATGAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCCCGGCAtt                                                                   >  1:155132/1‑143 (MQ=255)
                                                                          aTCGCAATCGAGTGACTCATCCTCGTAGCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCGTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTaa                                                                 <  1:408892/143‑1 (MQ=255)
                                                                               aaTCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTggg                                                            <  1:304562/143‑1 (MQ=255)
                                                                                 tCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGGTGTCGATTTACTGGCAATCCCGCCATTAAGTGGGTg                                                          >  2:385893/1‑143 (MQ=255)
                                                                                          tCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGCTGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGCTTTGCTTc                                                 >  1:69666/1‑143 (MQ=255)
                                                                                               ttcttATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTTTCTATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACAtc                                            >  1:352322/1‑143 (MQ=255)
                                                                                                tcttATCCTCATCAGTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACCGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACAtct                                           <  1:66126/143‑1 (MQ=255)
                                                                                                  ttATCCTCATCATTTTTCGTCGCGTCACATCTACGACGAGATGAGTGTAAAAATCGTGCTGTCAATTAACCTTTCGCCTGTTGCCGCCAGTGTCGATTTACTGGCAATCACAGCATTAAGAGGGTGATTTGCTTcaaaccact                                         >  2:877200/1‑136 (MQ=255)
                                                                                                      ccTCATCATTTTGCGGCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGCCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCa                                     <  1:909009/143‑1 (MQ=255)
                                                                                                        tcatcaTTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTCAGTGGGTGATTCGCTTCACACCTCCGGCAtt                                   >  2:704374/1‑143 (MQ=255)
                                                                                                        tcatcaTTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTAACGCGGTGGTACCTTTGGCGTGTTGCCGCCGTTGTCGATTTACTGTCAATCACGGCATTACGTGGCTGATTTGCTACACATCTCTGGCCtt                                   >  2:417200/1‑143 (MQ=255)
                                                                                                           ccgtttttCGTCGCGTCACACCTCCTACGAGATGGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTc                                <  2:621725/140‑1 (MQ=255)
                                                                                                             atTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCt                              >  1:612600/1‑143 (MQ=255)
                                                                                                              tttttCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATCTGCATCACATCTCCCGCATTTTCCTg                             >  2:147389/1‑143 (MQ=255)
                                                                                                                 ttCGTCGCGTCACATCTCCGACGAGATGGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCaa                          <  1:88028/143‑1 (MQ=255)
                                                                                                                 ttCGTCGCGTCACATCTCCGACGAGATGGGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCaa                          <  1:88006/143‑1 (MQ=255)
                                                                                                                   gggtgcgTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCaaaa                        <  1:724674/139‑1 (MQ=255)
                                                                                                                     tcccgccacaTCTCCGACGAGATGAGCGTAAAACTCGTGCAGTCGATTAACCTTTCGCCTGTTGCCGCCGTGATCGACTTCCTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAAcc                      <  1:133989/137‑1 (MQ=255)
                                                                                                                     gcgcgTCACATCTCCGACGAGATGGGTGTAAAAAACGTGCTGTCGACTAAACTTTCGACTGTTGAAGCCGTTGTAGATTTCCTGGCAATGACGACATTAAGCAGCTGAATCGCTTAAACTCTCGGGCATTTTCCTGCAAAAcc                      <  2:875824/142‑1 (MQ=255)
                                                                                                                             caTCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCtt              >  1:540747/1‑143 (MQ=255)
                                                                                                                             caTCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCtt              <  1:785872/143‑1 (MQ=255)
                                                                                                                              aTCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGGTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTGGGGCATGTTACTGAAAAACCAAAACCTTa             >  2:39951/1‑143 (MQ=255)
                                                                                                                              aTCTCCGACGAGATGAGTGTAAAAATCGTGCTATCGATTAACCTTTCGCCAGTTGCCGCCGTTGTCGATTCACTAGCAATCACGGCATTAAGTGGGTGATTTGCTTCCCATCTCGGGCACTCTCCTTCAGAACCATACCCtcc             >  2:158699/1‑141 (MQ=255)
                                                                                                                               tctcCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCTTAc            <  1:413226/143‑1 (MQ=255)
                                                                                                                                    gtcgaGATGGGTGTAGAAATCGTGCTTTCGATTAACCTTTCGCCTGTTGTCGCTGTTGTCGATTTACTCGCAATCACGTCACTAAGTGGGTGATTTGCTGCACATCTCGGGCATTTTCCTGGAAGACCATACCCTTACGaaaa       <  2:352628/141‑1 (MQ=255)
                                                                                                                                     acgaGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAGAACCATACCCTTACGAAAAg      >  1:563180/1‑143 (MQ=255)
                                                                                                                                        ataTGAGTGTAAAAATCGTGCTGTCGATTAACCTGTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCTTACGAAAAGTAc   <  1:6750/141‑1 (MQ=255)
                                                                                                                                         gaTGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCTTACGAAAAGTACg  >  2:348532/1‑143 (MQ=255)
                                                                                                                                             |                                                                                                                                          
ATTTTTTTACTTTTTTGAACGGAGCGTAAAAACAGGCTGCACTGGCCGCGCCGATCAAATGCCAAAATATCCCCATCGTAATCGCGTTACTCATCTTCTTATCCTCATCATTTTTCGTCGCGTCACATCTCCGACGAGATGAGTGTAAAAATCGTGCTGTCGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTTCACATCTCGGGCATTTTCCTGCAAAACCATACCCTTACGAAAAGTACG  >  NC_000913/4100432‑4100711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑