Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,434,8820TG48.9% 62.6 / 14.3 48Y252S (TAC→TCC) truAtRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (5/19);  new base G (23/0);  total (29/19)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCAT  >  NC_000913/2434735‑2435030
                                                                                                                                                   |                                                                                                                                                     
ggTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCCGGCAGGGGaa                                                                                                                                                     >  2:279444/1‑150 (MQ=255)
ggTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAAt                                                                                                                                                    <  2:786446/151‑1 (MQ=255)
 gTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGaaac                                                                                                                                                   >  2:366484/1‑149 (MQ=255)
 gTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGGCAGGGGAAt                                                                                                                                                    >  1:163205/1‑150 (MQ=255)
   ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGGCAGGGGAATcc                                                                                                                                                  >  2:98156/1‑150 (MQ=255)
     atatTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATTATACCAGTCCGGGGAAACCa                                                                                                                                                 >  1:511135/1‑149 (MQ=255)
            ccTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACGGGCAGGGGAAACCACCGCGAcc                                                                                                                                         >  2:335745/1‑150 (MQ=255)
              tATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACCGGCAGGGGAATACAcccccac                                                                                                                                          >  1:313835/1‑142 (MQ=255)
               aTGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATAATAACCGGGACGGGAATCCACCGCGGCCAg                                                                                                                                       >  1:505966/1‑149 (MQ=255)
                tGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATAATACCGGGCCGGGGAAACCCCCGCGACCCGa                                                                                                                                      >  1:705158/1‑149 (MQ=255)
                 gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCCGTCAGGGGAATCCACCGCGACCAGAt                                                                                                                                     >  2:201332/1‑149 (MQ=255)
                   cTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATACACCGCGACCAGATa                                                                                                                                    >  1:463156/1‑148 (MQ=255)
                    ttGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATTCACCGCGACCAGATACa                                                                                                                                  >  2:126436/1‑149 (MQ=255)
                             tCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATAACGGTCAGGGGAATCCACCGCGACCAGATACAGC‑CCCTcc                                                                                                                         >  2:655528/1‑148 (MQ=255)
                                    tCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGcc                                                                                                                <  2:315342/150‑1 (MQ=255)
                                     cAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGt                                                                                                              <  1:836173/151‑1 (MQ=255)
                                           gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTtgctg                                                                                                         <  1:366446/150‑1 (MQ=255)
                                             aaCTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCCGGCAGGGGAATCCACCGCGACCAGATAAAGC‑CCCTCCCCCTTTTCCGTTTCTgcc                                                                                                       >  1:805167/1‑150 (MQ=255)
                                                 aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTgccgcta                                                                                                   <  2:246370/150‑3 (MQ=255)
                                                  cGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATAACCGTCAGGGGAAACCACCGCGGCCCGATACAGC‑CCTTCCGCTTTTTCCGTTGCTgcccccccc                                                                                                 >  1:129644/1‑148 (MQ=255)
                                                   gTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCAGGGAAATTCACCGCGGCCCGAAACAGC‑CCCTCCGCTTTTTCCCTTGCTGCCCCCcgcg                                                                                                >  2:809556/1‑151 (MQ=255)
                                                       gCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATGCCCGTCACGGGAATCCACCGCGGCCCGAAACAGCACCTTCC‑CTTTTTCCCATTCTGCCCCCCGccctct                                                                                            >  2:843755/1‑146 (MQ=255)
                                                          aCAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTg                                                                                           <  2:338050/149‑1 (MQ=255)
                                                           cAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTcc                                                                                        <  1:10417/151‑1 (MQ=255)
                                                            aGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATATAGC‑CCCTTCCCTTTTTTCGGTTCTGCCGCCCGCGTTTTGTcc                                                                                        >  1:157332/1‑150 (MQ=255)
                                                                tGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCCGGCAGGGGAATCCACCCCGACCCGATACAGC‑CCCTTCTCTTTTTTCGTTTCTGCCGCCCGCGGTCTTTCCttt                                                                                     >  2:639368/1‑149 (MQ=255)
                                                                     tGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCGGTCAGGGGAAACCACCCCGACCAGATAAAGC‑CCTTCCGCCTTTTCCGGTTGTGCCCCCAGCGGTCTGTCCCTTtccgcc                                                                               >  1:65404/1‑150 (MQ=255)
                                                                      gTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAg                                                                             <  2:705230/151‑1 (MQ=255)
                                                                             gCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAActc                                                                       <  2:718702/150‑1 (MQ=255)
                                                                              cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGC‑CCCTCCCCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTCCTTTTCCGCCCGCAActc                                                                       >  2:313049/1‑149 (MQ=255)
                                                                               attattCTCGTTAGTCCGCCAGAAATAGGGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGGTCTGTCCTTTGCCGCCAGCCAc                                                                         >  1:150841/1‑146 (MQ=255)
                                                                                 tattCTCGTTAGTCCGCCAGAAATAGGGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCt                                                                   <  2:150874/150‑1 (MQ=255)
                                                                                       cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGc                                                            <  1:143823/151‑1 (MQ=255)
                                                                                       cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCCCGACCAGATACAAC‑CCTTCCCCTTTTTCCCTTTCTGCCGCCCGCGTTCTGTCCTTTTCCCCCCGCAACTCTGCTTTCCCGc                                                            >  2:65100/1‑151 (MQ=255)
                                                                                         ttAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAATTCATCCCCGTCACGGTAATCCACCCCGACCCGATACAGC‑CCCTCCGCTTTTGCCGTTGCTGCCGCCAGCCGTCTGTACTTTTCCGCCCGCCACTCCTCTATCCacacc                                                          >  1:74665/1‑147 (MQ=255)
                                                                                                gCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCAGGGGAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTTCCGGTGGTGCCGCCCGCGTTTTGTCCTTTGCCCCCCGCCAACCTGCTATACAGCTCTCCgg                                                     >  1:777751/1‑149 (MQ=255)
                                                                                                    gAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGtt                                               <  2:546270/151‑1 (MQ=255)
                                                                                                             ggCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCAcc                                      <  1:489513/151‑1 (MQ=255)
                                                                                                               cccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGa                                    <  1:639301/151‑1 (MQ=255)
                                                                                                                        ggTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                            >  1:610828/1‑150 (MQ=255)
                                                                                                                        ggTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCa                           <  2:145685/151‑1 (MQ=255)
                                                                                                                           tttGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAgg                         <  2:594232/150‑1 (MQ=255)
                                                                                                                               gAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGcc                    <  1:481207/151‑1 (MQ=255)
                                                                                                                                 aGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg                   >  1:630174/1‑150 (MQ=255)
                                                                                                                                    tCATACCGTTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGAc                 <  2:475626/149‑1 (MQ=255)
                                                                                                                                      aTACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAat              >  2:575429/1‑150 (MQ=255)
                                                                                                                                      aTACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAat              >  2:870376/1‑150 (MQ=255)
                                                                                                                                                 ggTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCat  <  1:669506/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                     
GGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGC‑CCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCAT  >  NC_000913/2434735‑2435030

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑