Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,074,524 T→C 7.4% I14V (ATC→GTC)  PP_5692 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,074,5240TC 7.4% 153.9 / 2.8 54I14V (ATC→GTC) PP_5692hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (29/21);  new base C (2/2);  total (31/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

GCGGTTAGGTTCGCCCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCC  >  NC_002947/5074379‑5074665
                                                                                                                                                 |                                                                                                                                             
gCGGTTAGGTTCGCCCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGAtctc                                                                                                                                            >  8:265986/1‑149 (MQ=255)
  ggTTAGGTTCGCCCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTcgc                                                                                                                                          <  7:265986/149‑1 (MQ=255)
              ccGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTGGCTCaa                                                                                                                                >  5:272576/1‑147 (MQ=255)
              ccGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGACCGCGAGATCGCTctgat                                                                                                                              <  5:337437/149‑5 (MQ=255)
               cGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGACCGCGAGATCGCTctgatg                                                                                                                             <  3:359370/149‑6 (MQ=255)
                    gCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCAt                                                                                                                        >  1:289889/1‑149 (MQ=255)
                      ccTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGc                                                                                                                      >  1:3120/1‑149 (MQ=255)
                          ggTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTc                                                                                                                    <  7:295775/147‑1 (MQ=255)
                                aaTCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGAt                                                                                                            >  4:288648/1‑149 (MQ=255)
                                        cAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTACTTCAGTCACAATCAGAGCGATCTCTCGGTCGCTCAACAGTCCATGCTCAATGGGATAAACGccc                                                                                                    >  7:147224/1‑149 (MQ=255)
                                         aaGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCGATGCTCAATGGGATTCACGCCCt                                                                                                   >  2:23760/1‑149 (MQ=255)
                                            gATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCtttt                                                                                                <  8:129131/149‑1 (MQ=255)
                                            gATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCtttt                                                                                                >  3:190441/1‑149 (MQ=255)
                                                 cccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCcg                                                                                           >  2:124903/1‑149 (MQ=255)
                                                  ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATggg                                                                                                              <  6:358264/129‑1 (MQ=255)
                                                  ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCCCGCCCTGTTCCCcgc                                                                                          >  4:348600/1‑149 (MQ=255)
                                                  ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCCGTCGCTCAACAGGCCATGCTCAATggg                                                                                                              >  5:358264/1‑129 (MQ=255)
                                                      tCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTc                                                                                      <  4:190441/149‑1 (MQ=255)
                                                         tGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAg                                                                                    >  1:220066/1‑148 (MQ=255)
                                                              ggCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTTAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAatat                                                                              <  8:40578/149‑1 (MQ=255)
                                                                 gcACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATAttt                                                                            >  3:359991/1‑148 (MQ=255)
                                                                  cacaGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTga                                                                          <  1:23760/149‑1 (MQ=255)
                                                                          cATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTcc                                                                  <  6:304391/149‑1 (MQ=255)
                                                                           aTCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTcc                                                                  >  2:303013/1‑148 (MQ=255)
                                                                            tCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                <  3:288648/149‑1 (MQ=255)
                                                                              cATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACa                                                              >  5:250509/1‑149 (MQ=255)
                                                                                tttATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACAt                                                             >  4:100501/1‑148 (MQ=255)
                                                                                tttATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATc                                                            <  2:3120/149‑1 (MQ=255)
                                                                                    taGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCAcag                                                        >  2:242342/1‑147 (MQ=255)
                                                                                      gATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGcc                                                      <  1:303013/149‑1 (MQ=255)
                                                                                      gATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTAACGCCCTTTACCCCGCCCTCAGCAATATTTGAGAATTTCCGACATCAACGca                                                      >  4:5882/1‑148 (MQ=255)
                                                                                             gAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGc                                               >  7:220859/1‑149 (MQ=255)
                                                                                                 ccgccgCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTGGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCt                                           <  6:272576/149‑1 (MQ=255)
                                                                                                    ccgcAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCtttt                                        <  6:250509/149‑1 (MQ=255)
                                                                                                      gcAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTg                                       >  6:6650/1‑148 (MQ=255)
                                                                                                       cAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTa                                     <  2:220066/149‑1 (MQ=255)
                                                                                                            gCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCt                                 >  4:152217/1‑148 (MQ=255)
                                                                                                                tATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                >  5:64475/1‑113 (MQ=255)
                                                                                                                tATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                <  6:64475/113‑1 (MQ=255)
                                                                                                                    aaGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGACCTTTTCCCCGCTCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCtt                        <  1:242342/149‑1 (MQ=255)
                                                                                                                         gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCtt                        >  8:142652/1‑144 (MQ=255)
                                                                                                                         gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCtt                        <  7:142652/144‑1 (MQ=255)
                                                                                                                         gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGaa                     >  2:85237/1‑147 (MQ=255)
                                                                                                                         gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACa                   <  3:100501/149‑1 (MQ=255)
                                                                                                                          tAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAg                  <  4:153365/149‑1 (MQ=255)
                                                                                                                          tAGTTCAGACCCCATCAGAGCGATCTCGAGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGAGCTCAGCAATATTTGAGAATTTCCGACATCACAGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAg                  >  7:262711/1‑149 (MQ=255)
                                                                                                                             ttCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGACAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCt               >  8:170666/1‑149 (MQ=255)
                                                                                                                                    cccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCAc                                                                                                        >  5:84706/1‑53 (MQ=255)
                                                                                                                                    cccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCAc                                                                                                        <  6:84706/53‑1 (MQ=255)
                                                                                                                                     ccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGttt       >  2:315176/1‑149 (MQ=255)
                                                                                                                                       tgttgagCGACCGCGAGATCGCTCAACAGGCCATGCTCAATGGGATTCACGCGCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTc     >  3:242219/5‑149 (MQ=255)
                                                                                                                                        tCAGATCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCg    <  5:6650/149‑1 (MQ=255)
                                                                                                                                        gttgagCGACCGCGAGATCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCg    >  4:227298/4‑149 (MQ=255)
                                                                                                                                           gagCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGcc  >  6:144351/1‑148 (MQ=255)
                                                                                                                                           gagCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGcc  >  4:137879/1‑148 (MQ=255)
                                                                                                                                                 |                                                                                                                                             
GCGGTTAGGTTCGCCCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTGTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCC  >  NC_002947/5074379‑5074665

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: ‑