Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913925,9000AG42.9% 91.3 / 13.8 56noncoding (72/88 nt)serWtRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (2/30);  new base G (24/0);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 7.46e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGA  >  NC_000913/925757‑926048
                                                                                                                                                 |                                                                                                                                                        
aCTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGaa                                                                                                                                                    >  2:135663/1‑150 (MQ=255)
    ccGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAccccc                                                                                                                                               <  1:513803/151‑1 (MQ=255)
     cGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCg                                                                                                                                              <  1:369944/151‑1 (MQ=255)
      gTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGa                                                                                                                                             <  1:264875/151‑1 (MQ=255)
       tACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAAacccc                                                                                                                                               >  1:167810/1‑148 (MQ=255)
             cAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCCATACGtt                                                                                                                                       >  1:488217/1‑150 (MQ=255)
                  tAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCg                                                                                                                                   <  2:574765/149‑1 (MQ=255)
                            caGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACttt                                                                                                                     <  2:188992/151‑1 (MQ=255)
                             aGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCCGTACGTTGCCGTATAAACACttt                                                                                                                     >  2:485861/1‑150 (MQ=25)
                             aGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTCGACCCCCCCAAACATTGCCGtcttcaaccatt                                                                                                                       >  1:651535/1‑139 (MQ=25)
                                 aaCATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAg                                                                                                                 <  1:637519/151‑1 (MQ=255)
                                        tCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCGATACGGTGCCGTATACACACTTTTCCGGCg                                                                                                              >  2:574333/1‑146 (MQ=21)
                                        tCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTTCCGTATACACACTTTTCCGGCg                                                                                                              >  2:47435/1‑146 (MQ=21)
                                               gCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAACCCCCCCTACGTTTGCGTATACACACCTTTCAGGCGGGCTCCTTCAGc                                                                                                  >  2:42589/1‑151 (MQ=18)
                                                  caccaTGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGAGGGGGGGTTGGGCCCCCGCTACGATGCCCTATAAAAACATTCCAAGCGTGCTCCTTTCGCCAc                                                                                               >  1:77441/1‑151 (MQ=18)
                                                        gTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGTACCCCCGACACGTTTCCGTATACACACTTTCCAGGCGGGCTCCTTCAGCCACTccgg                                                                                          >  1:466568/1‑147 (MQ=17)
                                                        gTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGac                                                                                         <  2:506026/151‑1 (MQ=255)
                                                          tCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTCGGACCCCCCATACCTTTCCGTTTACACACTTTTCCGGGCGGGTCCTTCCCCCACTccggc                                                                                         >  1:93056/1‑145 (MQ=17)
                                                             cTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCt                                                                                    <  2:255635/150‑1 (MQ=255)
                                                                    acagacagATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCCGCCACTCGGACACCTCACCaaa                                                                            <  1:151637/150‑1 (MQ=255)
                                                                    acagacagATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAt                                                                           <  1:498676/151‑1 (MQ=255)
                                                                         cagaTAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTGCCGTATACACACTTTTCAGGCGGGCTCCTTCAGCCCCCCGGACACCCCACCAAAATGttt                                                                      >  2:526701/1‑151 (MQ=14)
                                                                           gaTAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTTGAACCCCCCCTACGTTGCCGTATACACACTTTCCCGGGGGGGTCCTTCCGCCCCCCCGGCACCCCCCCCAAATtttttt                                                                     >  1:282136/1‑151 (MQ=14)
                                                                                 aTGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAACCCCCCCAACGTTGCCGTATACACACTTTCCAGGCGGGCTCCTTCAGCCACCCCGACACCCCCCCCAAATGTTTTGCTAcc                                                               >  1:55193/1‑150 (MQ=14)
                                                                                  tGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGAACCCCCCATACGTTGCCGTATAAACACTTTTCCGGCGTGCTCCTTCCGCCACTCGGACACCCCACCAAAAtttttt                                                                     >  2:677524/1‑143 (MQ=11)
                                                                                   gCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTTAGGGGGGGATTCTAACCCCCGATACGTTGCCGTATACCCACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCCCCAAATTGTTTTGCTACCaaa                                                            <  1:664585/151‑1 (MQ=255)
                                                                                        aaaaaaaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCATACGTTGCCGTATACACAATTTTCAGGCGTGGTCCTTCAGCCACTCGGGCACCCCACCCAAATGTTTTTTTTCCAAACCTc                                                        >  2:410585/1‑151 (MQ=14)
                                                                                         aaaaaaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCa                                                       <  1:172993/151‑1 (MQ=255)
                                                                                         aaaaaaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCa                                                       <  2:339415/151‑1 (MQ=255)
                                                                                             aaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTTGGGGGGGGGTTTGCAACCCCCATAAGTTTCCGTATACACACTTTTCAAGCGTGGGCCCTCAACCCCCCGGGCACCCCCCCCAATTTTTTTGGTAACAAACCTCATggg                                                   >  1:640633/1‑151 (MQ=9)
                                                                                              aGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTCGAAACCCCCCTACGTTGCCGTATACACACTTTCCAGGCGGGCTCCTTCAGCCACTCGGACACCCCACCCAAATGTTTTTCTACCAAAACCCATggg                                                   >  2:56501/1‑150 (MQ=14)
                                                                                                    cACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTTGGACCCCCCCCAACTTTCCCTATAAACACCTTTCCAGGGGGGTTCTTCCCCCCCCCGGGCACCCCACCAAAATGTTTTTCTACCAAACCTCCTGGGTGGcca                                             >  1:438468/1‑148 (MQ=9)
                                                                                                        ttCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGAGTAGAACCCCCCCTAAGTTGCCGTATACACACTTTTCAGGAGTGCTCCTTCAACCACCCCGACACCTCACCCAAATTTTTTTCTAACAAACCTCCTGGGGGGGAACgggg                                        >  2:328056/1‑151 (MQ=14)
                                                                                                         tCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACgggg                                        <  1:231997/150‑1 (MQ=255)
                                                                                                          cGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGgcg                                      <  1:38077/151‑1 (MQ=255)
                                                                                                          cGTACGAGCTCTTCTTGAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATCCGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGgc                                       <  1:530589/150‑1 (MQ=255)
                                                                                                           gTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGGTCGAAACCCCCATACGTTGCCGGAAACACACATTCCCGGCGTGCTCCTTCAGCCACTCGGGCACCCCACCAAAATGTTTTTCTACCCAAACCCATTGGGGGGAACgggg                                        >  2:215432/1‑148 (MQ=2)
                                                                                                            tACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTTGGAACCCCCCCACGTTTTCGTATACACACTTTTCCGGCGGGGTCCTTCACCCACCCGGGGACCCCACCAAAATTGTTTTCTTACACAACCCCTTGGGGGGAAAgggg                                         >  1:190975/1‑147 (MQ=2)
                                                                                                             aCGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGcta                                   <  2:389338/151‑1 (MQ=255)
                                                                                                                     ttcttTAAATATGGCGGTGAGGGGGGGGTTCGGACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCCCTCCGGCACCTCCCCAAAATTTTTTTCTTCCAAAACTCATTGGTGGCAACGGGGCGCCCCTATAggg                           >  2:84077/1‑151 (MQ=17)
                                                                                                                     ttcttTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCGCTACGTTTCCGGATACACACTTTCCAGGGGTGCTCCCTCCGCCACCCCGCCACCCCACCCAAATGTTTTTCTACCCAAACCCCTGGGGGGCAAAGGGGCGCCACtattagg                           >  2:4325/1‑147 (MQ=9)
                                                                                                                      tcttTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAg                             <  1:117746/148‑1 (MQ=255)
                                                                                                                       cgttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAggg                           <  2:583521/147‑1 (MQ=255)
                                                                                                                        tttAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCATACGTTGCCGGATACAAACTTTCCAGGCGTGCTCCTTCAGCCACCCGGACACCCCCCCCAAATGTTTTTCTTCCAAACCCCATGGGGGGGAACGGGGCGCTACTATAtgggg                         >  2:649350/1‑148 (MQ=17)
                                                                                                                         ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAg                         <  2:27583/149‑1 (MQ=255)
                                                                                                                           aaaTATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTgg                     <  2:93076/151‑1 (MQ=255)
                                                                                                                           aaaTATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTg                      <  1:485823/150‑1 (MQ=255)
                                                                                                                             atatGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTgg                     >  2:640061/1‑149 (MQ=255)
                                                                                                                                 ggCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTaa                <  1:37586/150‑1 (MQ=255)
                                                                                                                                  gCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTaaaa              <  2:94526/151‑1 (MQ=255)
                                                                                                                                  gCGGTGAGGGGGGGATTCGAACCCCCGATACGTGGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGt                  <  1:561098/147‑1 (MQ=255)
                                                                                                                                         aGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCa        <  2:601376/151‑1 (MQ=255)
                                                                                                                                             ggggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCaagaa    <  2:207527/151‑1 (MQ=255)
                                                                                                                                              gggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCaagaag   <  2:221724/151‑1 (MQ=255)
                                                                                                                                              gggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCaagaag   <  2:220199/151‑1 (MQ=255)
                                                                                                                                               ggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAagaaga  <  2:585827/151‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                        
ACTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGA  >  NC_000913/925757‑926048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: