Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,038,7950CG66.1% 49.9 / 73.1 62noncoding (1277/2905 nt)rrlA23S ribosomal RNA of rrnA operon
Reads supporting (aligned to +/- strand):  ref base C (13/8);  new base G (23/18);  total (36/26)
Fisher's exact test for biased strand distribution p-value = 7.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

GATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGC  >  NC_000913/4038646‑4038879
                                                                                                                                                     |                                                                                    
gATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCg                                                                                     <  1:394230/151‑1 (MQ=39)
         gggCTAAACCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAg                                                                            <  1:602256/151‑1 (MQ=39)
               aaCCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCt                                                                      <  2:660454/151‑1 (MQ=39)
                    tGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCg                                                                 >  2:742195/1‑151 (MQ=39)
                        ccGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGa                                                               >  2:653701/1‑149 (MQ=40)
                                gCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAg                                                       <  1:427520/149‑1 (MQ=40)
                                       cGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGt                                              <  2:295456/151‑1 (MQ=38)
                                       cGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGt                                              >  2:116547/1‑151 (MQ=38)
                                           acTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCa                                           <  2:626841/150‑1 (MQ=35)
                                             cgtaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGaaa                                                              >  2:260916/13‑129 (MQ=2)
                                             cgtaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGaaa                                                              <  1:260956/117‑1 (MQ=2)
                                              gtaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTgcg                                             >  1:12443/12‑143 (MQ=2)
                                                   tgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACACGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTgcgc                                            <  1:142546/135‑4 (MQ=2)
                                                   tgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACACGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTgcgc                                            >  2:142523/7‑138 (MQ=2)
                                                    gacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                                        >  1:109842/6‑128 (MQ=2)
                                                    gacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                                        <  2:109827/123‑1 (MQ=2)
                                                     gttgGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCgg                                <  1:473838/151‑1 (MQ=31)
                                                      cgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       <  1:271368/124‑1 (MQ=2)
                                                      cgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       >  2:271328/4‑127 (MQ=2)
                                                       tgGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCggg                               <  1:406316/150‑1 (MQ=31)
                                                        cggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAGCGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCgacgc                             >  1:112734/2‑147 (MQ=2)
                                                        cggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTcccgcgc                                            <  1:207306/135‑6 (MQ=2)
                                                        cggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTcccgcgc                                            >  2:207271/2‑131 (MQ=2)
                                                         ggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGAcc                                                          >  1:464707/1‑121 (MQ=2)
                                                         ggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGAcc                                                          <  2:464639/121‑1 (MQ=2)
                                                               ggAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       <  1:193340/118‑1 (MQ=2)
                                                               ggAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       >  2:193308/1‑118 (MQ=2)
                                                                gAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTg                       >  2:75015/1‑149 (MQ=31)
                                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAGTGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       <  2:62259/117‑1 (MQ=2)
                                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAGTGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       >  1:62270/1‑117 (MQ=2)
                                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAga                                                      >  1:257453/1‑117 (MQ=2)
                                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAga                                                      <  2:257413/118‑2 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGATAATGGGTGTGTAAAACACCCACGCCGAAAGAc                                                           >  1:480762/1‑111 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGATAATGGGTGTGTAAAACACCCACGCCGAAAGAc                                                           <  2:480694/111‑1 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCTAAAGACCAAgg                                                      >  2:340065/1‑116 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCTAAAGACCAAgg                                                      <  1:340114/116‑1 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      <  2:503947/116‑1 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      >  1:504018/1‑116 (MQ=2)
                                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTc                   >  2:148279/1‑151 (MQ=2)
                                                                   cGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCg                  >  1:586662/1‑151 (MQ=31)
                                                                    gTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCg                  >  2:263759/1‑150 (MQ=31)
                                                                    gTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      >  1:56884/1‑114 (MQ=2)
                                                                    gTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      <  2:56874/114‑1 (MQ=2)
                                                                    gTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCgg                 >  2:318355/1‑150 (MQ=2)
                                                                     ttCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGAc                >  1:372654/1‑151 (MQ=31)
                                                                      tCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGAcc               >  2:212857/1‑151 (MQ=31)
                                                                       cTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                             <  1:149257/104‑1 (MQ=2)
                                                                       cTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                             >  2:149234/1‑104 (MQ=2)
                                                                       cTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      <  2:291244/111‑1 (MQ=2)
                                                                       cTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      >  1:291288/1‑111 (MQ=2)
                                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAggga                                                    <  2:159531/111‑2 (MQ=2)
                                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAggga                                                    >  1:159555/1‑110 (MQ=2)
                                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       <  2:58038/108‑1 (MQ=2)
                                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                                       >  1:58048/1‑108 (MQ=2)
                                                                           aaGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTa           >  1:401009/1‑150 (MQ=31)
                                                                           aaGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTa           >  1:540848/1‑150 (MQ=31)
                                                                            aGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTa           >  1:226268/1‑149 (MQ=31)
                                                                              ccTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGc       >  2:388966/1‑151 (MQ=31)
                                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      <  1:231125/101‑1 (MQ=2)
                                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                                      >  2:231087/1‑101 (MQ=2)
                                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCGGTTCCTAAGGCg      >  2:253908/1‑149 (MQ=2)
                                                                                  tgAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGc  >  2:8794/1‑151 (MQ=11)
                                                                                                                                                     |                                                                                    
GATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGC  >  NC_000913/4038646‑4038879

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: