Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,781,1520AG22.7% 139.9 / 14.3 76intergenic (+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 (43/15);  new base G (0/17);  total (43/33)
Fisher's exact test for biased strand distribution p-value = 1.91e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCG  >  NC_000913/3781054‑3781250
                                                                                                    |                                                                                                   
ggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAg                                                                                                    <  2:162704/100‑1 (MQ=255)
ggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAg                                                                                                    >  2:1316153/1‑100 (MQ=255)
 gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAgg                                                                                                   >  2:246843/1‑100 (MQ=255)
  agagGGGACCGTTCGGCGCTGTATGTTCTCCCTCTCTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                                                                                  <  2:25587/100‑1 (MQ=255)
  agagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                                                                                  <  2:1533686/100‑1 (MQ=255)
  agagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                                                                                  <  2:308573/100‑1 (MQ=255)
     ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaa                                                                                              >  2:1805788/1‑100 (MQ=255)
     ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaa                                                                                              >  2:2049031/1‑100 (MQ=255)
     ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaa                                                                                              >  1:507244/1‑100 (MQ=255)
     ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaa                                                                                              >  2:366106/1‑100 (MQ=255)
      gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaaa                                                                                             >  1:1520488/1‑100 (MQ=255)
      gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGaaa                                                                                             <  1:70411/100‑1 (MQ=255)
      gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTGTCTCCCTCGCCCCTCCGTGGAGAGGGCCGCGGTGAGGGGaaa                                                                                             >  1:1559618/1‑100 (MQ=255)
        gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAg                                                                                           >  2:2161793/1‑100 (MQ=255)
                 gcgcTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTTTCCCTCTCTCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTg                                                                                  >  1:1179346/1‑100 (MQ=255)
                     tgtatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGGGAGGGGAAAAGGCCGCCCTGCTCa                                                                              >  2:38134/1‑100 (MQ=255)
                       tatgtcCCCCCTCCCTCTGAAACGACCCCGCCCTTTTTTTTCCCCCCCCCCCCCCCGGGGGGGGGGCCGGGGGGGGGGGAAAAAGGCCGCACTGCTCAc                                                                             <  1:2161781/99‑1 (MQ=255)
                         tgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCaa                                                                          >  2:1350998/1‑100 (MQ=255)
                         tgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCaa                                                                          >  2:1077047/1‑100 (MQ=255)
                           taCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAAtt                                                                        >  2:1384773/1‑100 (MQ=255)
                             cTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAAtttt                                                                      >  2:600680/1‑100 (MQ=255)
                               ccccccctctGAAACGACCCCGCCCTCTTTTTTCCCCCCCCCCCCCTCGGGGGAGGGGGCGGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    <  2:1389266/94‑1 (MQ=255)
                               cccTCACTCTGAAACGACACCGCGCTTTTTTTTTCCCCCTCGCCCCCCCGGGGGGGGGGCCGGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    <  1:168898/100‑1 (MQ=255)
                               cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    >  1:320727/1‑100 (MQ=255)
                               cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    >  1:323802/1‑100 (MQ=255)
                               cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    >  1:1482791/1‑100 (MQ=255)
                               cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                    >  1:396201/1‑100 (MQ=255)
                                 cccACTCTGAAACGACACCGCACTCTCTTCTTCTCCCTCGCCCCTCCGGGGATAGGGCCGGGGTGAGGGGCAAAGGCCGCACTGCTGACCAATTTTCTGc                                                                  >  1:527397/3‑100 (MQ=38)
                                 cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                  >  1:9527/1‑100 (MQ=255)
                                   ccctcgGAACCGCCCCCGCCCTCTTTTTTCCCCCCCCGCCCCCCGGGGGGGGGGCCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                  <  1:181313/96‑1 (MQ=255)
                                      gttGAACCTACACCGCCCTCTTTTTCTCCCCCTCCCCTACCGGGGGGGAGGGCAGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                                             <  2:1534937/98‑1 (MQ=255)
                                       ctacaaCGGCCCCGCCCTCTTTTTTTCTCCCTCGCCCCCCCGGGGAGAGGGCCGGGTTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                                             <  1:264759/95‑1 (MQ=255)
                                       ctGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCt                                                            >  1:1948949/1‑100 (MQ=255)
                                       cggAAACGACACCGCACTCTTTTTTTCTCCCGCGCCCCCCGGGGGAGGGGGCCGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                  <  1:2133748/92‑1 (MQ=255)
                                         gAAACGACACCGCACTCTTTTTTTCTTTTTTGTCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                                          >  1:1971310/1‑100 (MQ=255)
                                           aaactcacCGCCCTTTTTTTTTCCCCCCCCCCCCCCCGGGGAAGGGGCCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTa                                                                <  2:260328/88‑1 (MQ=255)
                                           aaCGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGccc                                                        >  1:386971/1‑100 (MQ=255)
                                                 acgaccccctTTTTTTGTCCCCCCCCCCACGGGGGAAGGGGCGGGGGTGTGGGTAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                                  <  2:1925484/92‑1 (MQ=255)
                                                  ccgtattttttttttCTCCCTCGCCCCGCGGGGGGGGGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCa                                                   <  1:946023/90‑1 (MQ=255)
                                                  ccGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                                  >  1:675204/1‑99 (MQ=255)
                                                  ccGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                                 >  2:1434647/1‑100 (MQ=255)
                                                    gccctctTTTTTTCTCCCTCCCCCCGCGGGGGGGGGGGCCGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                                  <  1:1229513/94‑1 (MQ=255)
                                                        tttttttttCCCCCCCGCCCCCCGGGGGGGAGGGCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAgggg                                           <  1:31402/98‑1 (MQ=255)
                                                         ctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                          >  1:73653/1‑100 (MQ=255)
                                                         ctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                          >  1:1880742/1‑100 (MQ=255)
                                                          ttttttcCCCCCTCCCCCCCCGGGGGGGGGGGCCGGGTGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGc                                         <  2:1520495/100‑1 (MQ=255)
                                                          ttttttcCCCCCCCCCCCCCCGGGGGGGGGGGCCGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                          <  1:61092/99‑1 (MQ=255)
                                                           ttttttCCCCCCCCCCCCCCCGGGGGGGGGGCCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGc                                         <  2:1249282/100‑1 (MQ=255)
                                                            tttttCCCCCCCGCCCCCTGGGGGAGGGGGCCGGCGCCAGCAGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAg                                       <  2:564936/100‑1 (MQ=255)
                                                             ttttCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGt                                      >  2:391877/1‑100 (MQ=255)
                                                             ttttCCCCCCCGGCCGCTCGGGGGGGGGGCCCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAg                                       <  1:1328526/100‑1 (MQ=255)
                                                                    ccccccccccccGGGGGGGGGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCt                                 <  1:1536847/93‑1 (MQ=255)
                                                                    ccTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAACGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaa                               >  1:821814/1‑100 (MQ=255)
                                                                     cTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                              >  2:2101630/1‑100 (MQ=255)
                                                                     cTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                              >  1:343733/1‑100 (MQ=255)
                                                                          ccccTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATc                          >  1:1578585/1‑100 (MQ=255)
                                                                          ccccGCGGGGGGGGGGGCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                                <  1:2068995/94‑1 (MQ=255)
                                                                            ccTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTTCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                        >  2:614281/1‑100 (MQ=255)
                                                                            ccTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                        >  2:1685489/1‑100 (MQ=255)
                                                                               cgggggAGGGGGCGGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTAc                      <  1:2084499/97‑1 (MQ=255)
                                                                                 ggggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACttt                   >  1:1539633/1‑100 (MQ=255)
                                                                                  ggggGAGGGCCGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTa                  <  1:391876/100‑1 (MQ=255)
                                                                                   ggAGGGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc                 <  1:1701281/100‑1 (MQ=255)
                                                                                   ggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc                 >  1:1976929/1‑100 (MQ=255)
                                                                                      gagGTCCGCGGCGAGGGGAACAGGCCGCACTGCCCACCAATTTTCTGCTATCCTGCCCCCGCACAAAGGGGGCCGTATGCTAAACATCGTACTTTAc                 >  1:1089662/1‑97 (MQ=255)
                                                                                        gggCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc            <  2:323803/100‑1 (MQ=255)
                                                                                        gggCGGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc            <  2:1595798/100‑1 (MQ=255)
                                                                                        gggCCGGGTGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc            <  1:2109175/100‑1 (MQ=255)
                                                                                          gCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg          >  2:1881176/1‑100 (MQ=255)
                                                                                          gCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg          >  2:1587875/1‑100 (MQ=255)
                                                                                           gcgggggggggggAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg          <  2:209108/97‑1 (MQ=255)
                                                                                              ggggTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGaaa       >  1:76069/1‑100 (MQ=255)
                                                                                                ggTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAAtt     <  2:1369627/100‑1 (MQ=255)
                                                                                                ggTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAAtt     >  1:782490/1‑100 (MQ=255)
                                                                                                  tGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTCTGCTCAACATCGTCCTTTACGAACCAGAAATTcc   >  1:2055175/1‑100 (MQ=255)
                                                                                                   gAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCg  <  2:315937/100‑1 (MQ=255)
                                                                                                   gAGGGCAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAAtt     <  1:366105/97‑1 (MQ=255)
                                                                                                    |                                                                                                   
GGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCG  >  NC_000913/3781054‑3781250

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: