Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,177,302 C→T 7.2% G228D (GGC→GAC)  PP_4553 ← ECF family RNA polymerase sigma‑70 factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,177,3020CT 7.2% 162.5 / 2.0 55G228D (GGC→GAC) PP_4553ECF family RNA polymerase sigma‑70 factor
Reads supporting (aligned to +/- strand):  ref base C (24/27);  new base T (2/2);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.82e-01

GCCTGGCGAACCAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACACGCTTTC  >  NC_002947/5177158‑5177450
                                                                                                                                                 |                                                                                                                                                    
gCCTGGCGAACCAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACTGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGAc                                                                                                                                                  <  2:265977/149‑1 (MQ=255)
 ccTGGCGAACCAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGAcc                                                                                                                                                 >  3:176897/1‑149 (MQ=255)
 ccTGGCGAACCAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGAcc                                                                                                                                                 <  4:176897/149‑1 (MQ=255)
        aaacAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACTAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCg                                                                                                                                          <  1:108265/146‑1 (MQ=255)
           cAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGt                                                                                                                                       >  5:138236/1‑149 (MQ=255)
           cAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGt                                                                                                                                       >  7:63321/1‑149 (MQ=255)
               gCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCggg                                                                                                                                   <  5:87896/149‑1 (MQ=255)
               gCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCggg                                                                                                                                   >  2:257816/1‑149 (MQ=255)
                cacaGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGgc                                                                                                                                  <  3:219417/149‑1 (MQ=255)
                   aGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGAcc                                                                                                                                                 >  5:169842/1‑131 (MQ=255)
                   aGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGAcc                                                                                                                                                 <  6:169842/131‑1 (MQ=255)
                     cccTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCaa                                                                                                                             <  8:63321/149‑1 (MQ=255)
                      ccTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAAc                                                                                                                            <  4:258830/149‑1 (MQ=255)
                      ccTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCAGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGgcgagaca                                                                                                                            >  6:166846/1‑143 (MQ=255)
                          ggCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCa                                                                                                                        >  5:169345/1‑149 (MQ=255)
                            cAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCAcc                                                                                                                      <  1:257816/149‑1 (MQ=255)
                             aaTGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCa                                                                                                                     <  6:169345/149‑1 (MQ=255)
                               ttcattGCCGGTCCCACAAGCTACGGTCCTGCTGCGTCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAg                                                                                                                    >  1:39974/6‑149 (MQ=255)
                                            ccACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGc                                                                                                      >  1:265729/1‑149 (MQ=255)
                                             cacaAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGc                                                                                                      >  3:64904/1‑148 (MQ=255)
                                             cacaAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCACGCCAGGc                                                                                                      >  2:56858/1‑148 (MQ=255)
                                              acaAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGa                                                                                                    <  2:164543/149‑1 (MQ=255)
                                                aaGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAAt                                                                                                  <  2:132217/149‑1 (MQ=255)
                                                  gCTAGGGTCCTGCTGC‑TCCATAACCACCAAATCGCGTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATgg                                                                                                <  4:64904/149‑1 (MQ=255)
                                                  gCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATgg                                                                                                <  3:218323/149‑1 (MQ=255)
                                                   cTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGc                                                                                               <  1:242545/149‑1 (MQ=255)
                                                      cGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCt                                                                                              <  2:66102/147‑1 (MQ=255)
                                                         tCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATc                                                                                         >  5:111158/1‑149 (MQ=255)
                                                           ctgctgC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGc                                                                                       >  2:216016/1‑149 (MQ=255)
                                                             gctgc‑tCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAgg                                                                                                       <  8:123027/131‑1 (MQ=255)
                                                             gctgc‑tCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAgg                                                                                                       >  7:123027/1‑131 (MQ=255)
                                                                 c‑tCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAgg                                                                                                       >  4:217886/1‑127 (MQ=255)
                                                                 c‑tCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAgg                                                                                                       <  3:217886/127‑1 (MQ=255)
                                                                       gAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGATGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCctgc                                                                            >  2:247443/1‑149 (MQ=255)
                                                                            accaAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTgcag                                                                       >  1:241885/1‑149 (MQ=255)
                                                                             ccaAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGTCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTgcag                                                                       >  2:109006/1‑148 (MQ=255)
                                                                             ccaAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGTCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTgcag                                                                       >  2:112941/1‑148 (MQ=255)
                                                                              caAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGTCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTgcagca                                                                     <  1:109006/149‑1 (MQ=255)
                                                                              caAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGTCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTgcagca                                                                     <  1:112941/149‑1 (MQ=255)
                                                                                taTCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACCCCAGCACGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAgt                                                                   <  2:162113/148‑1 (MQ=255)
                                                                                aaTCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAgt                                                                   <  5:86750/149‑1 (MQ=255)
                                                                                    gCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGtc                                                                <  5:103524/148‑1 (MQ=255)
                                                                                           ccATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCGGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGa                                                        <  6:138236/149‑1 (MQ=255)
                                                                                                 aTGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCACGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGc                                                  <  1:56858/149‑1 (MQ=255)
                                                                                                       gcCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAgt                                                                   >  8:151173/1‑126 (MQ=255)
                                                                                                        cccGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAg                                           <  8:245758/149‑1 (MQ=255)
                                                                                                                 gggACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGtt                                   >  5:179213/1‑148 (MQ=255)
                                                                                                                        cTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAacac                             >  4:49233/1‑147 (MQ=255)
                                                                                                                             gcaACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCg                                                                                                                                     <  3:182226/38‑1 (MQ=255)
                                                                                                                             gcaACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCg                                                                                                                                     >  4:182226/1‑38 (MQ=255)
                                                                                                                               aaCATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGAt                    <  3:247324/149‑1 (MQ=255)
                                                                                                                                     aaCGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCg              >  2:251991/1‑149 (MQ=255)
                                                                                                                                               ggCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACACGCtt    <  2:265729/149‑1 (MQ=255)
                                                                                                                                                gCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACCCGCttt   >  4:230628/1‑149 (MQ=255)
                                                                                                                                                gCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACACGCttt   >  1:270487/1‑149 (MQ=255)
                                                                                                                                                 ccGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACACGCTTTc  >  7:98925/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
GCCTGGCGAACCAGAGCACAGCCCTCGGCAATGAACTGCCGGTCCCACAAGCTACGGTCCTGCTGC‑TCCAGAACCACCAAATCGCCTTGGCCATCGATGCGCGCCCGCTGCCGGGACGCCTGCAGCAACATCAACGCCAGCAGGCCGACCGCCTCCGGGTCGGGCAGCAACTGCACCAGCAACCGCGCCAGGCGAATGGCTTCATCGCTCAGCGCCTGCTGCAGCAGTGTCTCGCCCGATGACGCCGAATAGCCCTCGTTGAACACCAGGTAGATCACCCGCAACACGCTTTC  >  NC_002947/5177158‑5177450

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: ‑