Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,831,983 G→T 7.8% K148N (AAG→AAT)  pvdS → alternative sigma factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,831,9830GT 7.8% 161.7 / 2.0 51K148N (AAG→AAT) pvdSalternative sigma factor
Reads supporting (aligned to +/- strand):  ref base G (24/23);  new base T (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TGCAGAACGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGCTCTCGCTTTTGCTTGCAGCGCT  >  NC_002947/4831838‑4832131
                                                                                                                                                 |                                                                                                                                                    
tgCAGAACGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAAc                                                                                                                                                  <  1:601485/150‑1 (MQ=255)
   aGAACGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTCCGTCCCTCTGCGGATGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTgg                                                                                                                                               <  2:759427/150‑1 (MQ=255)
     aaCGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGc                                                                                                                                             <  1:149803/150‑1 (MQ=255)
     aaCGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGc                                                                                                                                             <  2:732774/150‑1 (MQ=255)
             gCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGcc                                                                                                                                     <  2:629736/150‑1 (MQ=255)
                         ccacATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAATGAACTGGGCGTATCGCCGACCTTGGTCaa                                                                                                                         >  1:768608/1‑150 (MQ=255)
                         ccacATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAATGAACTGGGCGTATCGCCGACCTTGGTCaa                                                                                                                         >  1:768052/1‑150 (MQ=255)
                         ccacATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCaa                                                                                                                         >  1:116332/1‑150 (MQ=255)
                               aaaCCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCAt                                                                                                                   <  2:429888/150‑1 (MQ=255)
                                 aCCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACCGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGa                                                                                                                 >  2:826184/1‑150 (MQ=255)
                                  ccgcgccgcgCTGAATGACATCGCGGAGGGCTTGAACGAAGTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGAt                                                                                                                >  1:454532/1‑150 (MQ=255)
                                  ccgcgccgcgCGGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGAt                                                                                                                <  1:254407/150‑1 (MQ=255)
                                        cgcgcTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGa                                                                                                          <  2:783299/150‑1 (MQ=255)
                                               aaTGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTg                                                                                                   >  2:348631/1‑150 (MQ=255)
                                                     aTCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCAt                                                                                             >  1:904469/1‑150 (MQ=255)
                                                        gcgGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGc                                                                                          >  1:629598/1‑150 (MQ=255)
                                                                 ttGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACg                                                                                 >  1:572135/1‑150 (MQ=255)
                                                                   gaacgaacTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGc                                                                               <  2:116332/150‑1 (MQ=255)
                                                                        aacTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTc                                                                          >  1:94066/1‑150 (MQ=255)
                                                                            gccgccGCGCACCCGATATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCa                                                                      <  1:244434/150‑1 (MQ=255)
                                                                             ccgccgCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCcgc                                                                                                            >  1:608753/1‑111 (MQ=255)
                                                                             ccgccgCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCcgc                                                                                                            <  2:608753/111‑1 (MQ=255)
                                                                               gccgcGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGc                                                                   >  1:1101246/1‑150 (MQ=255)
                                                                                      aCCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGa                                                            <  2:904469/150‑1 (MQ=255)
                                                                                       cccGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGAt                                                           >  1:764300/1‑150 (MQ=255)
                                                                                         cGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGCCGGCCAGTCGCCAGGCCTGAAGATGa                                                         <  2:454532/150‑1 (MQ=255)
                                                                                         cGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGa                                                         >  2:513254/1‑150 (MQ=255)
                                                                                          gCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCCGGc                                                                   >  2:452108/1‑139 (MQ=255)
                                                                                          gCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGc                                                                   <  1:452108/139‑1 (MQ=255)
                                                                                           cTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACt                                                       <  2:333338/150‑1 (MQ=255)
                                                                                               gCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTgcaa                                                   <  1:835931/150‑1 (MQ=255)
                                                                                                 tttCGAGATGTACCGCCGTAATGGCTTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTgcaagc                                                 >  2:565575/1‑150 (MQ=255)
                                                                                                     gagaTGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAAc                                             <  1:826184/150‑1 (MQ=255)
                                                                                                         tGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGTATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCa                                         <  2:998046/150‑1 (MQ=255)
                                                                                                             ccGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGGCTGGGAGCAAACGCCAGAGc                                     >  2:758694/1‑150 (MQ=255)
                                                                                                              cGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCg                                    >  1:637403/1‑150 (MQ=255)
                                                                                                               gCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGa                                   >  2:1105433/1‑150 (MQ=255)
                                                                                                               gCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACAGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGa                                   >  2:975805/1‑150 (MQ=255)
                                                                                                                ccTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGaa                                  >  1:925708/1‑150 (MQ=255)
                                                                                                                      tGGCGTGCCGCAGAAGGACATTGCCACGGAACTGGGCGTATCGCCGACATTGGTCAAGTTCATGATCCTCGATTCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGa                            >  2:680227/1‑150 (MQ=255)
                                                                                                                      tGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGAc                                                        >  2:293615/1‑122 (MQ=255)
                                                                                                                      tGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGAc                                                        <  1:293615/122‑1 (MQ=255)
                                                                                                                       ggCGTGCCGCAGAAGGACATTGCCAATGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGAt                           <  2:768052/150‑1 (MQ=255)
                                                                                                                       ggCGTGCCGCAGAAGGACATTGCCAATGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGAt                           <  2:768608/150‑1 (MQ=255)
                                                                                                                       ggCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGAt                           <  1:348631/150‑1 (MQ=255)
                                                                                                                         cGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACATTCAGCATCGTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCg                         >  1:1050131/1‑150 (MQ=255)
                                                                                                                           tGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGct                       <  2:637403/150‑1 (MQ=255)
                                                                                                                              cGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGctctg                    <  1:565575/150‑2 (MQ=255)
                                                                                                                                     ggACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGCTCTCGCTTttg             <  2:629598/150‑1 (MQ=255)
                                                                                                                                              cAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGCTCTCGCTTTTGCTTGCAgcg    >  1:745138/1‑150 (MQ=255)
                                                                                                                                                aGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGCTCTCGCTTTTGCTTGCAGCGCt  >  1:1002874/1‑150 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
TGCAGAACGCCTCGCCCGAAGCCACCCACATAAACCGCGCCGCGCTGAATGACATCGCGGAGGCCTTGAACGAACTGCCGCCGCGCACCCGCTATGCTTTCGAGATGTACCGCCTTAATGGCGTGCCGCAGAAGGACATTGCCAAGGAACTGGGCGTATCGCCGACCTTGGTCAACTTCATGATCCGCGATGCGCTGGTGCATTGCCGCAAGACGGCCAGTCGCCAGGCCTGAAGATGACTGCAAGCAAACGCCAGAGCGAACCTGGATCGCTCTCGCTTTTGCTTGCAGCGCT  >  NC_002947/4831838‑4832131

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑