Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,170,450 C→A 9.3% R58S (CGC→AGC)  PP_3669 → LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,170,4500CA 9.3% 162.5 / 2.7 55R58S (CGC→AGC) PP_3669LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (21/28);  new base A (2/3);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTGGGCCTTTC  >  NC_002947/4170304‑4170598
                                                                                                                                                  |                                                                                                                                                    
tCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGc                                                                                                                                                    <  6:732/149‑1 (MQ=255)
  gACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCa                                                                                                                                                   <  1:177079/148‑1 (MQ=255)
   aCATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGc                                                                                                                                                 >  6:234891/1‑149 (MQ=255)
     aTGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCGGATCAGCAGCgg                                                                                                                                               <  1:173726/149‑1 (MQ=255)
     aTGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGGGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCGGATCAGCAGCgg                                                                                                                                               <  8:25994/149‑1 (MQ=255)
        aaCCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGAGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCg                                                                                                                                            <  6:113396/149‑1 (MQ=255)
                  tGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGaa                                                                                                                                  <  6:26561/149‑1 (MQ=255)
                       ttCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAacccac                                                                                                                             <  6:364223/149‑1 (MQ=255)
                             gCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTCTTCGACGACCCGCTCCTGATCCGCAGCGGCCGGGCCATGGAACCCACCACACg                                                                                                                       >  1:56264/1‑149 (MQ=255)
                               ccTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACggg                                                                                                                     <  4:302893/149‑1 (MQ=255)
                                   atgatCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCgg                                                                                                                                           >  6:156039/1‑123 (MQ=255)
                                   atgatCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCgg                                                                                                                                           <  5:156039/123‑1 (MQ=255)
                                       tCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGaa                                                                                                                                  >  3:215748/1‑128 (MQ=255)
                                       tCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGaa                                                                                                                                  <  4:215748/128‑1 (MQ=255)
                                         gAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCAt                                                                                                                                      <  2:206743/122‑1 (MQ=255)
                                         gAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCAt                                                                                                                                      >  1:206743/1‑122 (MQ=255)
                                         gAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATg                                                                                                                >  5:64321/1‑144 (MQ=255)
                                            cGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCtt                                                                                                        <  2:2416/149‑1 (MQ=255)
                                              cAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTg                                                                                                      <  8:276583/149‑1 (MQ=255)
                                                aCCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCt                                                                                                    >  3:178787/1‑149 (MQ=255)
                                                    gACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAAc                                                                                                >  5:262069/1‑149 (MQ=255)
                                                       ccGCGTGGGTGAAAAGCTGTTTATCACCCAATCCTCCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTgg                                                                                             <  6:304591/149‑1 (MQ=255)
                                                              ggTGATAAACAGCTTTTCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGc                                                                                      >  2:115104/1‑149 (MQ=255)
                                                               gTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGcc                                                                                     <  5:234891/149‑1 (MQ=255)
                                                                  aaaaGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCAt                                                                                   <  1:140135/148‑1 (MQ=255)
                                                                   aaaGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATg                                                                                  >  4:74904/1‑148 (MQ=255)
                                                                       cTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGt                                                                             <  4:178787/149‑1 (MQ=255)
                                                                             aTCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAg                                                                                                             >  8:219435/1‑111 (MQ=255)
                                                                              tCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGa                                                                           <  4:34147/144‑1 (MQ=255)
                                                                              tCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGa                                                                           >  3:34147/1‑144 (MQ=255)
                                                                                 cccAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATg                                                                                                                >  5:181230/1‑104 (MQ=255)
                                                                                 cccAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATg                                                                                                                <  6:181230/104‑1 (MQ=255)
                                                                                 cccAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCt                                                                   <  6:64321/149‑1 (MQ=255)
                                                                                           cGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGcc                                                         <  3:74904/149‑1 (MQ=255)
                                                                                           cGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGcc                                                         >  7:117971/1‑149 (MQ=255)
                                                                                             tCAGCGCCGGCCTCGCCGGCGTGCGCGAGCTGGTCGACGACCCGCTGGTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACTGGCCATGCAGATCTTTGCTGAACTGGGCCCGGGCATGGACGTGATTTCCGCTGCCATCAGCcgc                                                       <  2:99741/149‑1 (MQ=255)
                                                                                             tCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCcgc                                                       <  8:117971/149‑1 (MQ=255)
                                                                                                   ccgccCTCGCCCGCCTGCTCGAGCTGTTCGTCGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCGCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCcgc                                                 <  2:56264/149‑1 (MQ=255)
                                                                                                    cgccCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGc                                                                                                     >  2:232120/1‑96 (MQ=255)
                                                                                                    cgccCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGc                                                                                                     <  1:232120/96‑1 (MQ=255)
                                                                                                    cgccCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCcgcg                                                >  8:274595/1‑149 (MQ=255)
                                                                                                        cTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGtt                                            >  4:233593/1‑149 (MQ=255)
                                                                                                          cgcccgccTGCGCGAGCTGTTCGACGACCCGCTGCTGATCTGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGc                                                                                                               <  2:321119/80‑1 (MQ=255)
                                                                                                          cgcccgccTGCGCGAGCTGTTCGACGACCCGCTGCTGATCAGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGc                                                                                                               >  1:321119/1‑80 (MQ=255)
                                                                                                            cccgccTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGAc                                        <  6:262069/149‑1 (MQ=255)
                                                                                                                    cgcgAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCaa                                <  3:233593/149‑1 (MQ=255)
                                                                                                                      cgAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACa                              <  2:82676/149‑1 (MQ=255)
                                                                                                                             ttCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCaa                       >  8:256468/1‑149 (MQ=255)
                                                                                                                               cgacgaCCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTACCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACg                     >  1:206519/1‑149 (MQ=255)
                                                                                                                                gacgacCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCATTGCTGAACAGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCGGCAACgt                    >  7:54078/1‑149 (MQ=255)
                                                                                                                                  cgacCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGCGTTTTGCAGATCTTTGCTGAACAGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACgtgt                  <  1:115104/149‑1 (MQ=255)
                                                                                                                                      ccGCTGCGGATCAGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCg              >  8:129470/1‑149 (MQ=255)
                                                                                                                                           gcgtaTCAGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTgg         <  7:129470/145‑1 (MQ=255)
                                                                                                                                            ctgATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTgg         <  7:27203/148‑1 (MQ=255)
                                                                                                                                              gATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTGGGcc      >  3:282549/1‑149 (MQ=255)
                                                                                                                                                  cGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTGGGCCTTTc  >  7:134433/1‑149 (MQ=255)
                                                                                                                                                  cGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTGGGCCTTTc  >  7:281605/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                    
TCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCCCTCGCCCGCCTGCGCGAGCTGTTCGACGACCCGCTGCTGATCCGCAGCGGCCGGGCCATGGAACCCACCCCACGGGCCATGCAGATCTTTGCTGAACTGGGCCCGGCCATGGACGTGATTTCCGCTGCCATCAGCCGCGCCCGCGAGTTCGACCCGGCCAACAGCTGCAACGTGTTCCGCCTGGGCCTTTC  >  NC_002947/4170304‑4170598

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: ‑