Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,641,455 C→G 9.3% S373C (TCC→TGC)  PP_4951 → EmrB/QacA family drug resistance transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,641,4550CG 9.3% 158.9 / 7.0 54S373C (TCC→TGC) PP_4951EmrB/QacA family drug resistance transporter
Reads supporting (aligned to +/- strand):  ref base C (21/28);  new base G (2/3);  total (23/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

ATCGAACGGTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTGCGCCGGCGCACTGTTGG  >  NC_002947/5641313‑5641592
                                                                                                                                                |                                                                                                                                         
aTCGAACGGTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTGCATg                                                                                                                                       >  5:199724/1‑147 (MQ=255)
 tCGAACGGTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGAAGGGCATCCTGCAGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAg                                                                                                                                    >  1:326743/1‑149 (MQ=255)
     aCGGTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGGTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCa                                                                                                                                <  5:366305/149‑1 (MQ=255)
       ggTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTGCATGGAGTTCACt                                                                                                                              <  7:23626/149‑1 (MQ=255)
       ggTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACt                                                                                                                              <  1:40394/149‑1 (MQ=255)
        gTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTg                                                                                                                             >  6:182329/1‑149 (MQ=255)
         ttCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTGCATGGAGTTCACTGc                                                                                                                            <  6:199724/149‑1 (MQ=255)
             gCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGAt                                                                                                                         >  6:353080/1‑148 (MQ=255)
                   gCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCa                                                                                                                                     <  1:130912/130‑1 (MQ=255)
                   gCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCa                                                                                                                                     >  2:130912/1‑130 (MQ=255)
                   gCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAaca                                                                                                                    >  7:176776/1‑147 (MQ=255)
                         tcCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGACGGACCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGa                                                                                                              >  1:111648/1‑149 (MQ=255)
                            tCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGc                                                                                                           <  2:230524/147‑1 (MQ=255)
                            tCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGc                                                                                                           >  1:230524/1‑147 (MQ=255)
                              aCCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCa                                                                                                        <  8:11627/148‑1 (MQ=255)
                                  gTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGAt                                                                                                   <  8:176776/149‑1 (MQ=255)
                                     aTACCTTGCTGTTGGGCATCCTGCTGGGAAGCCTGGGCCTGGTGGACTAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTTGGCGCAGTTAACTCCATGCAGTTCACTACGATGAACACATTGACGCTCTTCGAtctc                                                                                                <  2:326743/149‑1 (MQ=255)
                                     aTACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGAtctc                                                                                                >  3:87394/1‑149 (MQ=255)
                                          ttGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTcgacga                                                                                           >  3:246505/1‑149 (MQ=255)
                                            gCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGacgacg                                                                                         >  7:173673/1‑149 (MQ=255)
                                              tGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGAcgc                                                                                        >  2:52607/1‑148 (MQ=255)
                                              tGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGAcgc                                                                                        >  8:153945/1‑148 (MQ=255)
                                                         ctgctgGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCcagcag                                                                            <  2:111648/149‑1 (MQ=255)
                                                          tgctgGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCagcagc                                                                           >  5:255509/1‑149 (MQ=255)
                                                            ctgGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCgg                                                                         <  3:205470/149‑1 (MQ=255)
                                                            ctgGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCg                                                                          <  5:37776/148‑1 (MQ=255)
                                                                cAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAAc                                                                     <  1:52607/149‑1 (MQ=255)
                                                                   gcctgggcctggTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGc                                                                  <  5:182329/149‑1 (MQ=255)
                                                                        ggcctggTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCctg                                                               <  7:153945/147‑1 (MQ=255)
                                                                          cctggTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGt                                                           <  5:204975/149‑1 (MQ=255)
                                                                          cctggTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGt                                                           <  2:94781/149‑1 (MQ=255)
                                                                              gtggACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCggt                                                       <  8:173673/149‑1 (MQ=255)
                                                                                ggACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCggtgg                                                     >  7:241700/1‑149 (MQ=255)
                                                                                 gACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCTATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCggtggt                                                    <  8:151132/149‑1 (MQ=255)
                                                                                         gAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAAc                                            >  5:27075/1‑149 (MQ=255)
                                                                                         gAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAAc                                            >  5:32272/1‑149 (MQ=255)
                                                                                              cccTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCggtggt                                                    <  4:283774/138‑1 (MQ=255)
                                                                                              cccTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCggtggt                                                    >  3:283774/1‑138 (MQ=255)
                                                                                               ccTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTc                                        >  4:212630/1‑149 (MQ=255)
                                                                                               ccTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTc                                        <  3:212630/149‑1 (MQ=255)
                                                                                                cTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCg                                       <  6:255509/149‑1 (MQ=255)
                                                                                                       gctgctGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAAc                                                                     <  5:227725/112‑1 (MQ=255)
                                                                                                       gctgctGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAAc                                                                     >  6:227725/1‑112 (MQ=255)
                                                                                                        cggctgTTTGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCt                               <  2:161481/147‑1 (MQ=255)
                                                                                                          gctgTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTgg                             <  6:32272/149‑1 (MQ=255)
                                                                                                           ctgTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTGATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTgg                             <  6:27075/148‑1 (MQ=255)
                                                                                                                 gTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGc                      >  8:174036/1‑149 (MQ=255)
                                                                                                                 gTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGc                      <  8:241700/149‑1 (MQ=255)
                                                                                                                    cAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTg                   >  4:269065/1‑149 (MQ=255)
                                                                                                                                   ggcttaGTGAACTCCATGCAGTTCACTGCGATTATCACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCGTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTGCGCCTGCGCACTGtt    <  4:87394/144‑1 (MQ=255)
                                                                                                                                   ggCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAATTGTCGCTGAGCCTGGGTGTGGCCTGCGCCGGCGCACTg      <  1:64134/147‑1 (MQ=255)
                                                                                                                                     cgcAGTGAACTCGATGCAGTTGACTGCGATGATCTCAGTGACGCTCATCGATCTCGACGACTCCTGCGCCAGGATCGGTAACAGCGTGGTGTCGGTGTTCGCGCAACTGTCGGTGAGCCTGGGTGTGGCCTGCGCCGGCGCAGTGTTgg  <  1:26416/149‑1 (MQ=255)
                                                                                                                                            aaCTGCATGGAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTGCGCCGgc            >  6:71427/1‑132 (MQ=255)
                                                                                                                                            aaCTGCATGGAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTGCGCCGgc            <  5:71427/132‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                         
ATCGAACGGTTCGGCTATCGCATCATCCTCACCGGTAATACCTTGCTGTTGGGCATCCTGCTGGCAAGCCTGGGCCTGGTGGACGAGCAGAC‑‑CCCTTATTGGCTGCTGTTGGTGCAACTTGGCCTTCTGGGCGCAGTGAACTCCATGCAGTTCACTGCGATGAACACAGTGACGCTCATCGATCTCGACGACGCCAGCGCCAGCAGCGGTAACAGCCTGCTGTCGGTGGTCGCGCAACTGTCGCTGAGCCTGGGTGTGGCCTGCGCCGGCGCACTGTTGG  >  NC_002947/5641313‑5641592

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: ‑