Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,738,377 C→A 8.4% L272L (CTG→CTT)  PP_1532 ← putative Phage integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,738,3770CA 8.4% 142.3 / 2.3 46L272L (CTG→CTT) PP_1532putative Phage integrase
Reads supporting (aligned to +/- strand):  ref base C (19/23);  new base A (2/2);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

TTGGAGGGCTGGCCCCCAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAA  >  NC_002947/1738229‑1738523
                                                                                                                                                    |                                                                                                                                                  
ttGGAGGGCTGGCCCCCAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGAc                                                                                                                                                    <  6:34668/149‑1 (MQ=255)
  ggAGGGCTGGCCCCCAGTGCGAGGCCAAGTTTCACTGCAGCCCGTTCACGGGCCGCGGCGAACACTTTGCTGATTGTGTTGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACa                                                                                                                                                   <  6:258352/148‑1 (MQ=255)
  ggAGGGCTGGCCCCCAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACa                                                                                                                                                   <  2:177398/148‑1 (MQ=255)
           gCCCCCAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTGTCAAAGCAcctgg                                                                                                                                           <  2:123810/147‑4 (MQ=255)
              cccAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTAACGGGCCGCGGCTAACTCTTTGATGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATcgcg                                                                                                                                      <  4:9359/149‑1 (MQ=255)
              accAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATcgcg                                                                                                                                      <  2:325461/148‑1 (MQ=255)
                cAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGc                                                                                                                                    <  3:152002/149‑1 (MQ=255)
                         gCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACa                                                                                                                                                   >  6:146654/1‑125 (MQ=255)
                         gCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACa                                                                                                                                                   <  5:146654/125‑1 (MQ=255)
                         gCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTa                                                                                                                           >  6:305320/1‑149 (MQ=255)
                           cAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTAt                                                                                                                          >  2:116497/1‑148 (MQ=255)
                              gTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACt                                                                                                                      >  8:3438/1‑149 (MQ=255)
                                          cccGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCt                                                                                                           >  4:58433/1‑148 (MQ=255)
                                            cGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAg                                                                                                        <  4:159174/149‑1 (MQ=255)
                                               tCACGGGCCGCGTCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTTGTGGTGCAACAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCaa                                                                                                              <  7:280400/140‑1 (MQ=255)
                                               tCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCTCGGCCACGCCGTATAACTTCACCCaa                                                                                                              >  8:280400/1‑140 (MQ=255)
                                                 aCGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGa                                                                                                   <  5:305320/149‑1 (MQ=255)
                                                    ggCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGc                                                                                                <  5:101986/149‑1 (MQ=255)
                                                              aaCTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGt                                                                                      >  4:136499/1‑149 (MQ=255)
                                                                   tttGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGc                                                                                 >  5:50165/1‑149 (MQ=255)
                                                                      gCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTgg                                                                              >  6:187206/1‑149 (MQ=255)
                                                                        tGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCTCCCGATCGCGGCAACGCCGTATCACTTCCCCCAAGCTCAGGCTGATGCATTCAAGCGTTACGCTGGTg                                                                            >  8:288442/1‑149 (MQ=255)
                                                                         gATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGc                                                                           >  4:269556/1‑149 (MQ=255)
                                                                                  gAGCATGATGGGAGATCCCGCCTTCGCGCGGCTAATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTa                                                                  <  4:299550/149‑1 (MQ=255)
                                                                                         atgGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGc                                                           <  3:151361/149‑1 (MQ=255)
                                                                                            ggAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGccc                                                         <  5:187206/148‑1 (MQ=255)
                                                                                             gagaTCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCa                                                                                          <  8:222262/114‑1 (MQ=255)
                                                                                             gagaTCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACACGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCa                                                                                          >  7:222262/1‑114 (MQ=255)
                                                                                                aTCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTc                                                    <  3:269556/149‑1 (MQ=255)
                                                                                                    cGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTg                                                             >  7:100255/1‑136 (MQ=255)
                                                                                                    cGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTg                                                             <  8:100255/136‑1 (MQ=255)
                                                                                                          cgcgcgGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTg                                            <  6:50681/147‑1 (MQ=255)
                                                                                                            cgcgGCTGATTGTCCGGTGGTGGTGCGCCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGgac                                         >  1:173136/1‑148 (MQ=255)
                                                                                                                gCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCt                                    >  5:297845/1‑149 (MQ=255)
                                                                                                                    aTTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCa                                 <  7:3438/148‑1 (MQ=255)
                                                                                                                                tggtgCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCAc                    <  3:58433/149‑1 (MQ=255)
                                                                                                                                    gCACCAGGTGCTTTGCCAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCa                >  3:318073/1‑149 (MQ=255)
                                                                                                                                     cACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGcc                                                          <  6:231059/106‑1 (MQ=255)
                                                                                                                                     cACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGcc                                                          >  5:231059/1‑106 (MQ=255)
                                                                                                                                        cAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATccc            <  7:86625/149‑1 (MQ=255)
                                                                                                                                         gggTGCTGTCAAAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCg           >  3:117938/2‑149 (MQ=255)
                                                                                                                                          ggTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCg           >  2:147122/1‑148 (MQ=255)
                                                                                                                                          ggTGCTGTCAAATCACCCGATCGCTGCAACGCCGTATCACTTCACCCAAGCTCAGGCTTATGCATTCCAGCGTTACGCTGGTGCTGATCCTTATCCTTGCCCCCGTCTTCGATTGga                                          <  6:238296/117‑1 (MQ=255)
                                                                                                                                          ggTGCTGTAAAAGCACCCGATCGCGGCAACGCAGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCACCGTCTTCGATTGga                                          >  5:238296/1‑117 (MQ=255)
                                                                                                                                           gTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGa         <  1:116497/149‑1 (MQ=255)
                                                                                                                                               tttGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAAc     >  2:248625/1‑149 (MQ=255)
                                                                                                                                                   aCAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGaa  <  7:269819/148‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
TTGGAGGGCTGGCCCCCAGGTCGAGGCCAAGTTTCACTGCAGCCCGGTCACGGGCCGCGGCGAACTCTTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAA  >  NC_002947/1738229‑1738523

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: ‑