Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,947,745 G→T 9.7% A116A (GCC→GCA)  PP_3483 ← type II secretion system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,947,7450GT 9.7% 123.2 / 2.9 41A116A (GCC→GCA) PP_3483type II secretion system protein
Reads supporting (aligned to +/- strand):  ref base G (16/21);  new base T (2/2);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

CCAGGTCGGCGGCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCT  >  NC_002947/3947597‑3947890
                                                                                                                                                    |                                                                                                                                                 
ccAGGTCGGCGGCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTggg                                                                                                                                                  <  1:516873/150‑1 (MQ=255)
 cAGGTCGGCGGCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGc                                                                                                                                                 >  2:485941/1‑150 (MQ=255)
    gTCGGCGGCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCaa                                                                                                                                              <  1:485941/150‑1 (MQ=255)
      cggcggCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGc                                                                                                                                                 <  1:45963/145‑1 (MQ=255)
      cggcggCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGc                                                                                                                                                 >  2:45963/1‑145 (MQ=255)
                       tAAAGCGGCCCGCCTTGCAGTACGTCATCGATCCAGTTCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGt                                                                                                                           <  2:202666/150‑1 (MQ=255)
                           gcggcgCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCGCAGCAACTGGCCGCCTTGCCCGATCACCACACATTCGCGCTTGAGGCCCTGTGCCAAGGCCAGCTTGTCGAAGCGTgggg                                                                                                                       >  1:593258/1‑150 (MQ=255)
                           gcggcgCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGTGCCAAGGCCAGCTTGTCGAAGCGTgggg                                                                                                                       >  1:593281/1‑150 (MQ=255)
                                    cTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCca                                                                                                              <  1:86507/150‑1 (MQ=255)
                                              gtcgtcGATCCAGGCCAGGCGAGCGGGGGCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAggctgtg                                                                                                    <  2:555892/150‑1 (MQ=255)
                                               tcgtcgATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAggctgtgg                                                                                                   >  2:111899/1‑150 (MQ=255)
                                                    gATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTc                                                                                              <  2:726516/150‑1 (MQ=255)
                                                      tCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGa                                                                                            <  1:198369/150‑1 (MQ=255)
                                                         aggccaggcGCGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTa                                                                                         <  2:822435/150‑1 (MQ=255)
                                                           gccaggcGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACg                                                                                       >  2:633445/1‑150 (MQ=255)
                                                                     cGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTTTTGCTGTCGAGTACGGGGTAATGCa                                                                             <  1:755145/150‑1 (MQ=255)
                                                                      ggggTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGTGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAg                                                                            <  2:593281/150‑1 (MQ=255)
                                                                      ggggTCGAAGGGGTCAGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACAGTCGCGCTTGAGGCACTGTGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAg                                                                            <  2:593258/150‑1 (MQ=255)
                                                                                         aaCACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCgg                                                         <  1:185879/150‑1 (MQ=255)
                                                                                              gCCCAGAAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGaa                                                    >  2:130787/1‑150 (MQ=255)
                                                                                               cccAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGCCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAg                                                   <  2:166496/150‑1 (MQ=255)
                                                                                                      aCTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCgg                                            >  2:388074/1‑150 (MQ=255)
                                                                                                        tGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCAAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCAAGCAGGCTGTGGCTGTCGGGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCgggg                                          <  2:121483/150‑1 (MQ=255)
                                                                                                            cggcTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGgtgt                                      >  1:851288/4‑150 (MQ=255)
                                                                                                              ccTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCg                                    >  2:146744/1‑150 (MQ=255)
                                                                                                               cTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGc                                   >  1:611422/1‑150 (MQ=255)
                                                                                                                ttGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGca                                  <  1:587261/150‑1 (MQ=255)
                                                                                                                ttGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGca                                  <  1:587313/150‑1 (MQ=255)
                                                                                                                       aTCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGGGTCGccggccagg                           >  2:232528/1‑150 (MQ=255)
                                                                                                                        tCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGcaggccaggc                          <  1:146744/150‑1 (MQ=255)
                                                                                                                                 aTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGc                                                                    <  1:668528/99‑1 (MQ=255)
                                                                                                                                 aTTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGc                                                                    >  2:668528/1‑99 (MQ=255)
                                                                                                                                  ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTgg                                                                                                                         <  2:210912/45‑1 (MQ=255)
                                                                                                                                  ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTgg                                                                                                                         >  1:210912/1‑45 (MQ=255)
                                                                                                                                  ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCgg                                            >  1:264173/1‑122 (MQ=255)
                                                                                                                                  ttCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCgg                                            <  2:264173/122‑1 (MQ=255)
                                                                                                                                     gcgcTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTaa                                                                                 >  2:73159/1‑82 (MQ=255)
                                                                                                                                     gcgcTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTaa                                                                                 <  1:73159/82‑1 (MQ=255)
                                                                                                                                       gcTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGa           <  1:633445/150‑1 (MQ=255)
                                                                                                                                           gAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCa                >  2:617041/1‑141 (MQ=255)
                                                                                                                                           gAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCa                <  1:617041/141‑1 (MQ=255)
                                                                                                                                                aCTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCt  >  2:415291/1‑150 (MQ=255)
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CCAGGTCGGCGGCGTGGGCCAGGTAAAGCGGCGCGCCTTGCAGTACGTCGTCGATCCAGGCCAGGCGAGCGGGGTCGAAGGGGTCGGCGAACACGCCCAGCAACTGGCCGCCTTGCTCGATCAGCACACATTCGCGCTTGAGGCACTGGGCCAAGGCCAGCTTGTCGAAGCGTGGGGTGCTGGCCAGCAGGCTGTGGCTGTCGAGTACGGGGTAATGCAGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCT  >  NC_002947/3947597‑3947890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑