Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,947,761 G→A 10.2% P96P (CCC→CCT)  PP_3483 ← type II secretion system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,947,7610GA10.2% 104.8 / 2.6 40P96P (CCC→CCT) PP_3483type II secretion system protein
Reads supporting (aligned to +/- strand):  ref base G (16/19);  new base A (2/2);  total (18/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.87e-01

CCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTT  >  NC_002947/3947613‑3947905
                                                                                                                                                     |                                                                                                                                                
ccaggcGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACg                                                                                                                                                  <  6:57681/149‑1 (MQ=255)
 caggcGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACgg                                                                                                                                                 >  4:197172/1‑149 (MQ=255)
   ggcGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGGCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGATCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACggg                                                                                                                                                <  1:259985/149‑1 (MQ=255)
    gcGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGt                                                                                                                                              <  2:125234/149‑1 (MQ=255)
        gCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATg                                                                                                                                          <  3:197172/149‑1 (MQ=255)
         cGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAATCGTGGTGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGc                                                                                                                                         <  3:48037/149‑1 (MQ=255)
                       tCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAg                                                                                                                           <  5:99910/149‑1 (MQ=255)
                       tCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAg                                                                                                                           <  2:285361/149‑1 (MQ=255)
                          gCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACAGGGTAATGCAGGGTCAGGCCCAGgcg                                                                                                                        >  2:280986/1‑149 (MQ=255)
                          gCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACAGGGTAATGCAGGGTCAGGCCCAGgcg                                                                                                                        >  2:285218/1‑149 (MQ=255)
                             aaCACGCCCAGCAACTGGCCGCCTTGCTCGATCCGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCg                                                                                                                     <  2:5035/149‑1 (MQ=255)
                              acacGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACAGGGTAATGCAGGGTCAGGCCCAGGCGCCgg                                                                                                                    <  1:285218/149‑1 (MQ=255)
                              acacGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACAGGGTAATGCAGGGTCAGGCCCAGGCGCCgg                                                                                                                    <  1:280986/149‑1 (MQ=255)
                                acGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGt                                                                                                                  >  5:238745/1‑149 (MQ=255)
                                  gCCCAGAAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTTGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTg                                                                                                                 >  3:248583/1‑148 (MQ=255)
                                   cccAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGaa                                                                                                               <  8:44391/149‑1 (MQ=255)
                                   cccAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGAGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGCGTg                                                                                                                 >  1:137952/1‑147 (MQ=255)
                                          aCTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCg                                                                                                        <  6:238745/149‑1 (MQ=255)
                                                       cacGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TAGAAGCATGGGGTGCTGGCCAGCACGCTGAGGCTGTCGAGTACGGGGTAATCCAGGGTCAGGCCCAGGCGCCGGGTGAAGGAGTCGGGGGTGTCGcagg                                                                                           >  8:94544/3‑149 (MQ=255)
                                                          gATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTcagggct                                                                                          <  6:23090/147‑7 (MQ=255)
                                                                cacacaTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGcaggccaggc                                                                                     >  5:335203/1‑146 (MQ=255)
                                                                cacacaTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGcaggccaggc                                                                                     <  6:335203/146‑1 (MQ=255)
                                                                 acacaTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGAGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTc                                                                                 >  7:288473/1‑149 (MQ=255)
                                                                   acaTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTc                                                                                 >  5:69625/1‑147 (MQ=255)
                                                                      ttCGCGGTGGAGGCAGTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCGGGCCAGCAGGGTGTGGCTGTCGAGTACGGGGTAATGCAGGGGCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAgg                                                                             <  8:288473/148‑1 (MQ=255)
                                                                      ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAgg                                                                                                                                      <  3:130154/91‑1 (MQ=255)
                                                                      ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAgg                                                                                                                                      >  4:130154/1‑91 (MQ=255)
                                                                            cTTGAGGCACTGGGCCAAGTCCAGCTTG‑TCGATGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACTGGGTAATGCAGGGTCAGGCCCATGCGCCGGGTGAAGGTGTCGGGTGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGa                                                                      <  4:248583/149‑1 (MQ=255)
                                                                                  gCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGgc                                                                >  3:56306/1‑149 (MQ=255)
                                                                                   cACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGgcg                                                               >  3:173415/1‑149 (MQ=255)
                                                                                                  aGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGTCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTg                                                <  4:338402/149‑1 (MQ=255)
                                                                                                                  tatctggtGGGCAGCAGGGTGTGGCTGTCGAGTTCGGGGTTATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGGAGGCCAGGCGTTCCTGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGc                                 <  3:94711/142‑1 (MQ=255)
                                                                                                                   gggTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGc                                 >  5:344010/1‑148 (MQ=255)
                                                                                                                         tGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCTAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCaggag                           >  1:125897/1‑148 (MQ=255)
                                                                                                                           gCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCTAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCaggag                           <  2:125897/146‑1 (MQ=255)
                                                                                                                                 agGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTgg                                   >  7:156742/1‑132 (MQ=255)
                                                                                                                                 agGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTgg                                   <  8:156742/132‑1 (MQ=255)
                                                                                                                                 agGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCgggg                  <  3:142224/149‑1 (MQ=255)
                                                                                                                                           tgtCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCaggag                           <  1:271083/130‑1 (MQ=255)
                                                                                                                                           tgtCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCaggag                           >  2:271083/1‑130 (MQ=255)
                                                                                                                                            gtCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGaaa       >  1:126754/1‑149 (MQ=255)
                                                                                                                                               gAGTTCGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAAttt    <  2:137952/149‑1 (MQ=255)
                                                                                                                                                 gTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAAttttt  >  1:211073/1‑149 (MQ=255)
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CCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTG‑TCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTT  >  NC_002947/3947613‑3947905

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: ‑