Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,325,511 T→A 11.3% noncoding (133/149 nt) PP_mr52 → PrrF ncRNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,325,5110TA11.3% 140.7 / 7.9 53noncoding (133/149 nt)PP_mr52PrrF ncRNA
Reads supporting (aligned to +/- strand):  ref base T (25/22);  new base A (3/3);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

ATCGGGGCAAAGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTCAGCCAGCAGCAAT  >  NC_002947/5325366‑5325655
                                                                                                                                                 |                                                                                                                                                
atCGGGGCAAAGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAAATTg                                                                                                                                               >  3:105569/1‑149 (MQ=255)
    gggCAAAGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCgg                                                                                                                                           <  4:19573/149‑1 (MQ=255)
       cAAAGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAAATTGCCGGGTc                                                                                                                                        <  4:105569/149‑1 (MQ=255)
         aaGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAAATTGCCGGGTcaa                                                                                                                                      <  1:294181/149‑3 (MQ=255)
         aaGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAAATTGCCGGGTcaa                                                                                                                                      <  4:214794/149‑3 (MQ=255)
              aTTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCttttttt                                                                                                                                 <  2:101892/149‑1 (MQ=255)
                    ggCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCtgt                                                                                                                           <  6:305277/149‑1 (MQ=255)
                           tGAGAATTGTTATTATTATCGCAACTGGTAGCGAGACTCGAAGGATAAGCAAAGAGCCACTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGAAATTTGCCGGGTCTTTTTTAGCCTGTGCCtat                                                                                                                     >  5:257379/1‑146 (MQ=37)
                                  tGTTATTATTATGGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTGATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGAt                                                                                                              <  6:257379/148‑1 (MQ=255)
                                      attattttCGCAACTTGTCCGGTTACTGGTTTGTTAATCTAAGACCCCCTTGTTCGGTATCTAATATTATCTCCTCATCATGCTAATGAAGGTTATTGTCCCGGGAATTTTCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAgc                                                                                                          <  6:5210/148‑1 (MQ=255)
                                       ttattatCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAgcgc                                                                                                        >  3:316757/1‑149 (MQ=255)
                                       ttattatCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAgcg                                                                                                         <  8:285379/148‑1 (MQ=255)
                                         attatCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCtttt                                                                                                                    <  2:290572/135‑1 (MQ=255)
                                         attatCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCA‑GATCAgggggt                                                                                                      >  1:290572/1‑143 (MQ=255)
                                             tCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGc                                                                                                  >  3:179708/1‑149 (MQ=255)
                                               gCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTg                                                                                                <  4:316757/149‑1 (MQ=255)
                                                                  gTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACaata                                                                                       <  6:248470/139‑1 (MQ=255)
                                                                  gTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACaata                                                                                       >  5:248470/1‑139 (MQ=255)
                                                                        tAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATc                                                                       >  2:89952/1‑149 (MQ=255)
                                                                             tAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATcgccgc                                                                  >  1:273493/1‑149 (MQ=255)
                                                                                      cTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACca                                                         >  8:236234/1‑149 (MQ=255)
                                                                                          ttCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACcacaca                                                     >  3:14989/1‑149 (MQ=255)
                                                                                          ttCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCCGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACcacaca                                                     >  1:231171/1‑149 (MQ=255)
                                                                                                   tcAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCgg                                                                                                                                           <  3:90657/54‑1 (MQ=255)
                                                                                                   tcAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCgg                                                                                                                                           >  4:90657/1‑54 (MQ=255)
                                                                                                   tcAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGcc                                            >  1:63906/1‑149 (MQ=255)
                                                                                                     aGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTc                                          >  5:244555/1‑149 (MQ=255)
                                                                                                     aGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTc                                          <  4:179708/149‑1 (MQ=255)
                                                                                                           tctcCTCGTCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAgg                                    >  3:185289/1‑149 (MQ=255)
                                                                                                               ctcATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCg                                <  2:296855/149‑1 (MQ=255)
                                                                                                                tcatcaGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCgg                               >  3:296814/1‑149 (MQ=255)
                                                                                                                       gCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTtcgctc                        >  7:126028/1‑149 (MQ=255)
                                                                                                                       gCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTtcgctc                        >  4:264999/1‑149 (MQ=255)
                                                                                                                       gCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCAAGGCTCGGTtcgctc                        >  5:89142/1‑149 (MQ=255)
                                                                                                                        cTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTtcgctcg                       <  1:89952/149‑1 (MQ=255)
                                                                                                                         tAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAgg                                    <  5:255620/135‑1 (MQ=255)
                                                                                                                         tAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAgg                                    >  6:255620/1‑135 (MQ=255)
                                                                                                                          aaTCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGc                                        >  1:261618/1‑130 (MQ=255)
                                                                                                                          aaTCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGc                                        <  2:261618/130‑1 (MQ=255)
                                                                                                                           aTCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTtcgctcgct                     >  4:56732/1‑147 (MQ=255)
                                                                                                                           aTCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGccc                    >  2:208799/1‑149 (MQ=255)
                                                                                                                           aTCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGcc                     <  4:296814/148‑1 (MQ=255)
                                                                                                                            tCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCa                   >  3:306868/1‑149 (MQ=255)
                                                                                                                                 gTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTca              <  4:14989/149‑1 (MQ=255)
                                                                                                                                 gTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTca              <  7:236234/149‑1 (MQ=255)
                                                                                                                                  aaaaagACCCGGCAAATTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTcag             >  1:308802/6‑149 (MQ=255)
                                                                                                                                    aTTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTcagc            <  3:153498/148‑1 (MQ=255)
                                                                                                                                       gACCCGGCAAATTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTcagccag         >  6:113338/1‑148 (MQ=255)
                                                                                                                                        aCCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTCAGCcagca       <  4:185289/149‑1 (MQ=255)
                                                                                                                                          ccGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCt                <  7:284709/138‑1 (MQ=255)
                                                                                                                                          ccGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCt                >  8:284709/1‑138 (MQ=255)
                                                                                                                                            ggCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTCAGCCAgcagca    >  1:637/1‑148 (MQ=255)
                                                                                                                                             gCAATTTGCCGGGTCTTTTTTTGCCCGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTCAGCCAGCAGCAAt  <  2:231171/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
ATCGGGGCAAAGGGATTGACGGCTAAATGAGAATTGTTATTATTATCGCAACTGGTCGCGAGACTGGTTGGATAAGCTAAGAGCCCCTGGTTCGGACTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTATTGACCCGGCAATTTGCCGGGTCTTTTTTTGCCTGTGCCTTTTCAGGATCAGCGCCGCAGCTGCGCACAATAATCCTGCTCCGGCATCGCCGCCGTGTACCACACATAATCAGCCTCGCCAGGCTCGGTTCGCTCGCCCACCTCAGCCAGCAGCAAT  >  NC_002947/5325366‑5325655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑