Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,781,1520AG29.6% 109.7 / 24.3 72intergenic (+135/‑63)lldD/trmLL‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base A (33/17);  new base G (0/21);  total (33/39)
Fisher's exact test for biased strand distribution p-value = 9.30e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

GGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGC  >  NC_000913/3781053‑3781251
                                                                                                       |                                                                                                   
gggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGa                                                                                                     >  2:1515169/1‑100 (MQ=255)
gggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGa                                                                                                     >  2:2196540/1‑100 (MQ=255)
  gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAgg                                                                                                   <  1:2258625/100‑1 (MQ=255)
  gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAgg                                                                                                   <  1:2333596/100‑1 (MQ=255)
  gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAgg                                                                                                   >  2:810367/1‑100 (MQ=255)
   agagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                                                                                  <  1:1186674/100‑1 (MQ=255)
      ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggggca                                                                                               >  2:1111631/1‑98 (MQ=255)
      ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaa                                                                                               <  1:1515168/100‑1 (MQ=255)
         gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAg                                                                                            <  2:100690/100‑1 (MQ=255)
         gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAg                                                                                            >  2:1435080/1‑100 (MQ=255)
          aCCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAgg                                                                                           <  1:1215585/100‑1 (MQ=255)
          aCCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAgg                                                                                           <  2:1968821/100‑1 (MQ=255)
           ccGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAgg                                                                                           <  1:1381751/99‑1 (MQ=255)
                      tgtatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTTTTTTTCTCCTCAGAGGAGAGGGAAGGGTTGAGAGGAAAAGGCCGCACTGCTCa                                                                               >  2:293572/1‑100 (MQ=255)
                        tttgtcCTCCCTCACTCGAAAAGGCCCCCGCTCTTTTTTTTCCCCCCCGCCCCCCGGGGGGGGGGCGCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCa                                                                            <  1:1906583/98‑1 (MQ=255)
                        tatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGGGAGGGGAAAAGGCCGCACTGCTCAcc                                                                             >  1:2177415/1‑100 (MQ=255)
                          tgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCaa                                                                           >  1:43313/1‑100 (MQ=255)
                                cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                     >  2:19582/1‑100 (MQ=255)
                                cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                     >  1:1991004/1‑100 (MQ=255)
                                cccTCACACTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGAGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                     >  2:1267670/1‑100 (MQ=255)
                                 ccgcgctcgGAACCGAGACCGCAGTTTTTTTTCCGCCCCCCCCCCCCCGGGGAGAGGCCCGGGGAGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg                                                                    <  2:573724/95‑1 (MQ=255)
                                  ctctctctAAAACCCCCCCGCCCTTTTTTTTCCCCCCCCCCCCCTCGGGGGGGGGGGCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCtcc                                                                   <  1:1620631/100‑3 (MQ=255)
                                  cTCCCTCTGAAACGACCCCGCCCTCTTTTTTTCTCCCCCCCCCCCCGGGGGGGGGGGCGGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                   <  2:382283/100‑1 (MQ=255)
                                  cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                   >  1:959202/1‑100 (MQ=255)
                                      ttttGAAACTACCCCGCCCTCTTTTTTCCCCCCCCCCCCCCCCGGGGAGAGGCCCGGGTTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATc                                                               <  2:105880/97‑1 (MQ=255)
                                      ctctGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATc                                                               >  1:1791186/1‑100 (MQ=255)
                                        ctGAAACGCCCCCCCACTTTTTTTTTCCCCCCCCCCCCCCGGGGGAGGGGGCCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTAt                                                                <  1:2356623/97‑1 (MQ=255)
                                         tGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcaga                                                            >  1:105881/1‑97 (MQ=255)
                                         tGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTg                                                            >  2:1190479/1‑100 (MQ=255)
                                         tGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTg                                                            >  1:1847227/1‑100 (MQ=255)
                                          gAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                                           >  1:1183087/1‑100 (MQ=255)
                                          gAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                                           >  1:549931/1‑100 (MQ=255)
                                           aaaCGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcc                                                          >  1:2200888/1‑100 (MQ=255)
                                              cGACCCCGCCCTTTTTTTTCCCCCCCCCCCCCCCGGGGGGGGGGCCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcccc                                                        <  1:810367/99‑1 (MQ=255)
                                              cGACCCCGCACTCTTTTTTCCTCCCGCGCCCCTCCGGGGGGAGGGCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTg                                                            <  2:1902842/95‑1 (MQ=255)
                                              cGACACCGCACTCGTTTTTTCTCCCTCGCCCCTCCGGGCAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGccccc                                                       >  2:1482060/1‑100 (MQ=255)
                                                acacCGCACTCTTTTTTTCTGCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCg                                                      >  2:1464831/1‑99 (MQ=255)
                                                acacCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGAAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGc                                                     >  1:1688418/1‑100 (MQ=255)
                                                   ccGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                                  >  1:598378/1‑100 (MQ=255)
                                                   ccGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                                  >  2:2131145/1‑100 (MQ=255)
                                                   ccGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                                  >  1:2286430/1‑100 (MQ=255)
                                                    cGCCCTCTTTTTTCCCCCCCCGCCCCCCCGGGGAGAGGGCGGGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTa                                                 <  2:2200886/100‑1 (MQ=255)
                                                        ctctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                                             >  1:1516781/1‑100 (MQ=255)
                                                         tctTTTTTTCTCCCGCGCCCCGCGGGGGAGAGGCCTGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                                             <  1:1165616/99‑1 (MQ=255)
                                                          ctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                           >  1:1743874/1‑100 (MQ=255)
                                                           tttttttCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTTAGGGGAAAAGGCCGCACTCCTCACCAATTTTTTGCTATCCTGCCCCCGCACTAAgggg                                            >  2:665755/1‑98 (MQ=255)
                                                           ttttttcCCCCCCCGCCTCCCGGGGGGGGGGCCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAgggg                                            <  2:1847227/98‑1 (MQ=255)
                                                           ttttttcCCCCCCCGCCCCGCGGGGGAGGGGCCGGGGTGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                           <  1:1346437/99‑1 (MQ=255)
                                                            ttttttCCCCCGCGCCCCGCGGGGGAGGCGCCGGGCGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                                             <  2:1688419/96‑1 (MQ=255)
                                                                    cccTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                                 >  1:2006005/1‑100 (MQ=255)
                                                                    cccTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                                 >  2:683389/1‑100 (MQ=255)
                                                                    cccGCGCCCCTCGGGGGAGGGGGCGGGTGTGGGGGTAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                                 <  1:1111628/100‑1 (MQ=255)
                                                                     cctccgccccccGGGGGGGGGGCCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGc                                   <  1:1190477/92‑1 (MQ=255)
                                                                     ccTCGCCCCGCCGGGGAGAGGGCGGGGGTGTGGGCAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaa                                <  1:300276/100‑1 (MQ=255)
                                                                      cTCGCCCCTCCGAGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                               >  1:1573029/1‑100 (MQ=255)
                                                                        ttccgatctggggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACa                             <  1:722364/91‑1 (MQ=255)
                                                                        cGCCCCTCGGGGGGGGGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAAc                              <  1:1267669/99‑1 (MQ=255)
                                                                          ccccTCCGGGGAGGGGACCGGGGTAAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATg                                    <  2:20958/91‑1 (MQ=255)
                                                                           ccccccGGGGGGGGGGCGGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCg                          <  1:1518029/100‑1 (MQ=255)
                                                                            ccccgggggAGAGGGCCGGGGTGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                         <  2:1519178/95‑1 (MQ=255)
                                                                            ccaccGGGGGGGGGCCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                         <  1:19582/97‑1 (MQ=255)
                                                                             cccgggggAGGGGGCGGGGGTGGGGGCAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                         <  1:1402692/95‑1 (MQ=255)
                                                                                 ggggAGGGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACtt                     <  1:1212725/99‑1 (MQ=255)
                                                                                 ggggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACaagatcggaa                    >  2:722365/1‑91 (MQ=255)
                                                                                 ggggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACttt                    >  1:579483/1‑100 (MQ=255)
                                                                                  gggggggggCGGGGGTGGGGGCAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTa                   <  1:622209/94‑1 (MQ=255)
                                                                                  ggggGAGGGCCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                         <  2:2177413/94‑1 (MQ=255)
                                                                                    gggggggCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACg                 <  1:1482059/96‑1 (MQ=255)
                                                                                        gggCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGaa               <  2:92276/98‑1 (MQ=255)
                                                                                         ggCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAc              <  2:959204/98‑1 (MQ=255)
                                                                                          gCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg           <  2:2377604/100‑1 (MQ=255)
                                                                                          gCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg           >  2:633620/1‑100 (MQ=255)
                                                                                                gggTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAAt       <  2:1417514/100‑1 (MQ=255)
                                                                                                      gAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCg   >  1:1187315/1‑100 (MQ=255)
                                                                                                       aGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGc  >  2:2390652/1‑100 (MQ=255)
                                                                                                       |                                                                                                   
GGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGC  >  NC_000913/3781053‑3781251

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: