Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,249,749 A→T 7.8% intergenic (+22/+49) bvgA → / ← PP_1091 virulence factors transcription regulator BvgA/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,249,7490AT 7.8% 152.7 / 3.1 51intergenic (+22/+49)bvgA/PP_1091virulence factors transcription regulator BvgA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (25/22);  new base T (2/2);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01

GCCGACAGCATGTACCTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTCTTTGCGATT  >  NC_002947/1249605‑1249897
                                                                                                                                                 |                                                                                                                                                     
gCCGACAGCATGTACCTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTccagcc                                                                                                                                                    <  8:194783/148‑1 (MQ=255)
         aTGTACCTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCttt                                                                                                                                          <  1:50320/149‑1 (MQ=255)
            taacTCACTAACAAGACGGTCAGTACCTACAACGCACGGCCGCCGCTCAAGCTCAATGCACCGTCCTTGGTGGCCCTGATCGAGCTGGCGCAACGGCCAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCTGGCTGGAGGCttcaa                                                                                                                                        <  1:241746/146‑4 (MQ=255)
              ccTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAg                                                                                                                                     <  8:262152/149‑1 (MQ=255)
              ccTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAg                                                                                                                                     <  3:243961/149‑1 (MQ=255)
                tCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAggg                                                                                                                                   >  6:87391/1‑149 (MQ=255)
                    tAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTAt                                                                                                                               >  3:62420/1‑149 (MQ=255)
                       cAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCgg                                                                                                                            >  4:142904/1‑149 (MQ=255)
                          gACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGc                                                                                                                                        <  3:5692/134‑1 (MQ=255)
                          gACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGc                                                                                                                                        >  4:5692/1‑134 (MQ=255)
                          gACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTcc                                                                                                                         <  4:62420/149‑1 (MQ=255)
                           aCGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCa                                                                                                                        <  4:157195/149‑1 (MQ=255)
                              gTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGa                                                                                                                     <  3:142904/149‑1 (MQ=255)
                                            gTCACGGCTGCTGCTCAAGCTCAAAGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCa                                                                                                      >  7:113992/1‑149 (MQ=255)
                                             tCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCAc                                                                                                     <  2:101762/149‑1 (MQ=255)
                                               aCGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTa                                                                                                   >  3:283692/1‑149 (MQ=255)
                                                  gctgctgctCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAg                                                                                                <  6:217281/149‑1 (MQ=255)
                                                         ctcaagctcaaTGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTaa                                                                                         >  4:310691/1‑149 (MQ=255)
                                                          tcaagctcaaTGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAAt                                                                                        >  2:224904/1‑149 (MQ=255)
                                                                             aTTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCtt                                                                     >  2:275252/1‑149 (MQ=255)
                                                                              ttGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTACCGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCtt                                                                     <  1:224904/149‑1 (MQ=255)
                                                                                tgTTGACCTGATCGATCTGTCTCTTGGT‑CAAGGTCTGAACTGATCGCCAAGGCTTGAAGCCTCCAGCGAGGAGGCTTTGCCAGGGCTATCGGTGCATGTCTA‑CTGGACCCGCACTTCAGGTAGTAATCGAAATCGGCCAAGTGCTTCt                                                                   <  8:113992/147‑1 (MQ=255)
                                                                                  ttGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAg                                                                                                                                     <  8:152348/81‑1 (MQ=255)
                                                                                  ttGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAg                                                                                                                                     >  7:152348/1‑81 (MQ=255)
                                                                                     aCCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGgc                                                             >  7:16842/1‑149 (MQ=255)
                                                                                         gATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCAt                                                                                                                       >  3:301057/1‑88 (MQ=255)
                                                                                         gATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCAt                                                                                                                       <  4:301057/88‑1 (MQ=255)
                                                                                         gATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCg                                                         >  5:39089/1‑149 (MQ=255)
                                                                                          aTCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATTGAAATCGGCCAACTGCTTCTGCAGGCGCCGt                                                        >  5:45820/1‑149 (MQ=255)
                                                                                          aTCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGt                                                        >  4:11693/1‑149 (MQ=255)
                                                                                           tCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAggg                                                                                                                                   <  4:195779/74‑1 (MQ=255)
                                                                                           tCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAggg                                                                                                                                   >  3:195779/1‑74 (MQ=255)
                                                                                                    cgcAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCa                                              <  1:275252/149‑1 (MQ=255)
                                                                                                     gcAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCAt                                             >  5:134305/1‑149 (MQ=255)
                                                                                                       aaCGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCAtga                                           >  8:209166/1‑148 (MQ=255)
                                                                                                          gg‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCAtgttgt                                        <  6:39089/149‑1 (MQ=255)
                                                                                                                      aaCTGATCGCCAAGCCTTGAATCCTCCAGCCAGGAGGCTTTGCAAGGGCTATCGGTCCATGACTA‑CGGGACCCGAACTACACGTCGTAATCGAAATCTGCCAACTGCTTCTGCAGGAGCCCTTCTTCCAGAATGTTGACCATCGTGCGa                             >  4:100588/1‑149 (MQ=255)
                                                                                                                      aaCTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGa                             >  2:250452/1‑149 (MQ=255)
                                                                                                                       aCTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGAc                            >  3:54555/1‑149 (MQ=255)
                                                                                                                        cTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACg                           >  7:298464/1‑149 (MQ=255)
                                                                                                                            tCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTg                       <  3:11693/149‑1 (MQ=255)
                                                                                                                            tCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTg                       <  3:310691/149‑1 (MQ=255)
                                                                                                                                 aaGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGAAGTTTGCTAAg                  >  8:133503/1‑149 (MQ=255)
                                                                                                                                        gAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTc           >  1:104865/1‑149 (MQ=255)
                                                                                                                                        aaaGCCTCCTGGCTGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGc                               >  3:29568/2‑129 (MQ=255)
                                                                                                                                        aaaGCCTCCTGGCTGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGc                               <  4:29568/128‑1 (MQ=255)
                                                                                                                                        aaaGCCTCCTGGCTGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGCACCCGCACTACAGGTGGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTc           >  4:109896/2‑149 (MQ=255)
                                                                                                                                           gCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTCttt        <  2:104865/149‑1 (MQ=255)
                                                                                                                                            ccTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTCTTTg       <  4:283692/149‑1 (MQ=255)
                                                                                                                                            ccTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTCTTTg       <  8:16842/149‑1 (MQ=255)
                                                                                                                                              tCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAAc                                                                          <  8:3525/80‑1 (MQ=255)
                                                                                                                                              tCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAAc                                                                          >  7:3525/1‑80 (MQ=255)
                                                                                                                                                 agccagGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCATGTTGGTCTTTGCGAtt  <  3:100588/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                     
GCCGACAGCATGTACCTCAGTAACAAGACGGTCAGTACCTACAAGTCACGGCTGCTGCTCAAGCTCAATGCACGGTCATTGGTTGACCTGATCGAGCTGGCGCAACGG‑CAAGGTCTGAACTGATCGCCAAGCCTTGAAGCCTCCAGCCAGGAGGCTTTGCCAGGGCTATCGGTCCATGACTA‑CGGGACCCGCACTACAGGTCGTAATCGAAATCGGCCAACTGCTTCTGCAGGCGCCGTTCTTCCAGCATGTTGTCGATGGTGCGACGTTTGCTCAGGTTGGTCTTTGCGATT  >  NC_002947/1249605‑1249897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑