Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,346,435 T→C 8.8% E22G (GAG→GGG)  PP_2942 ← two‑component system response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,346,4350TC 8.8% 119.9 / 2.5 46E22G (GAG→GGG) PP_2942two‑component system response regulator
Reads supporting (aligned to +/- strand):  ref base T (19/22);  new base C (2/2);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CCCGTCCATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCATTTTTCC  >  NC_002947/3346287‑3346576
                                                                                                                                                    |                                                                                                                                             
cccGTCCATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGAct                                                                                                                                               >  5:195724/1‑149 (MQ=255)
  cGTCCATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGActcc                                                                                                                                             <  7:304232/149‑1 (MQ=255)
   gTCCATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTTGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGActcct                                                                                                                                            >  2:166265/1‑149 (MQ=255)
      cATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCtcgt                                                                                                                                         >  5:35035/1‑149 (MQ=255)
      cATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCtcg                                                                                                                                          <  4:245013/148‑1 (MQ=255)
                 tGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCACCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGGCTGCTAAGGATCGACTCCTCGTCGTCCACTAGc                                                                                                                              <  2:390557/149‑1 (MQ=255)
                    gcgcATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACCCCTCGTCGTCCACTAGCaa                                                                                                                            >  4:125856/1‑148 (MQ=255)
                    gcgcATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACCCCTCGTCGTCCACTAGCAac                                                                                                                           >  4:131815/1‑149 (MQ=255)
                     cgcATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAaca                                                                                                                          <  6:195724/149‑1 (MQ=255)
                            cTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCgg                                                                                                                   >  6:51976/1‑149 (MQ=255)
                                  aCCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCg                                                                                                                    >  6:299539/1‑142 (MQ=255)
                                  aCCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCg                                                                                                                    <  5:299539/142‑1 (MQ=255)
                                  aCCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATa                                                                                                             <  8:35117/149‑1 (MQ=255)
                                          aaCCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAgggtggg                                                                                                      <  1:257843/148‑1 (MQ=255)
                                             cGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTgggttcg                                                                                                  >  6:71319/1‑149 (MQ=255)
                                             cGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACGCCTCGTCGTCCACTAGCAACACGGTCGGCCGCTAGGGTgggttcg                                                                                                  >  1:334487/1‑149 (MQ=255)
                                                  ccgcGGCCATGTGCGGCTGTGCTTGTTCGTCGCTGGTCGCCTGCTTGACGTCATAGGGTTGGCGACGCAATAGCCGACGCAGACTGCTTATTATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTgggttcgggttc                                                                                             <  8:111026/146‑1 (MQ=255)
                                                      ggCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGgttcgggttcgg                                                                                           <  5:20602/147‑1 (MQ=255)
                                                         cATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCa                                                                                      >  1:186160/1‑149 (MQ=255)
                                                                  cAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATgg                                                                             >  8:267166/1‑149 (MQ=255)
                                                                    gTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATgg                                                                             >  4:169949/1‑147 (MQ=255)
                                                                       ccTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAgg                                                                         <  7:267166/148‑1 (MQ=255)
                                                                           ttCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTTGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCa                                                                    <  1:166265/149‑1 (MQ=255)
                                                                               ccgcTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCAcgcg                                                                >  7:145235/1‑149 (MQ=255)
                                                                                 gcTGGGCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGt                                                              <  8:197939/149‑1 (MQ=255)
                                                                                         ccAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTcgatcgat                                                      >  5:196929/1‑149 (MQ=255)
                                                                                         ccAGCTTCACGTCATAGGGTTGCCCACGCAATACCCTACGAATACTGCTATGTATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTcgatcgat                                                      <  7:273006/149‑1 (MQ=255)
                                                                                            gCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGa                                                   <  6:35035/149‑1 (MQ=255)
                                                                                             cTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACCCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAg                                                  <  3:131815/149‑1 (MQ=255)
                                                                                             cTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACCCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAg                                                  <  3:125856/149‑1 (MQ=255)
                                                                                                   gTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTc                                            >  7:148685/1‑149 (MQ=255)
                                                                                                   gTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTc                                            >  5:121831/1‑149 (MQ=255)
                                                                                                    tCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCg                                           <  2:21418/149‑1 (MQ=255)
                                                                                                      aTAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCAGGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAg                                         >  4:224373/1‑149 (MQ=255)
                                                                                                                 cACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAgcg                              <  8:148685/149‑1 (MQ=255)
                                                                                                                 cACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAAAACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACCCGGTCGATCGAAGGAGGCACTCGAGCTCAACCAgcg                              >  2:250160/1‑149 (MQ=255)
                                                                                                                    gCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCtt                           <  2:186160/149‑1 (MQ=255)
                                                                                                                     cAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCt                            >  3:10745/1‑147 (MQ=255)
                                                                                                                     cAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTa                          <  1:250160/149‑1 (MQ=255)
                                                                                                                            cGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCaaa                   <  4:10745/149‑1 (MQ=255)
                                                                                                                                 cAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGc                >  2:350563/1‑147 (MQ=255)
                                                                                                                                 cAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTa              <  5:71319/149‑1 (MQ=255)
                                                                                                                                  ataCTGCTAAGGATCGACTCCTCGTCATCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAg             <  3:319960/147‑1 (MQ=255)
                                                                                                                                        cTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCAtt       >  6:51831/1‑149 (MQ=255)
                                                                                                                                        cTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCAtt       >  4:365493/1‑149 (MQ=255)
                                                                                                                                         tAAGGATCGACTCCTCGTGGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGATAGATCAttt      >  4:393762/1‑149 (MQ=255)
                                                                                                                                             gATCGACTCCTCGTCGTCCACTAGCAACCCGGTCGGCCGCTAGGGGGGGTTCGGGGTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGCTGGAGGCACTCGAGCTCAACGATCGCTTAGGTCAAAGGCTAGATCATTTTTcc  <  8:145235/149‑1 (MQ=255)
                                                                                                                                                  aCTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCAttt      <  6:167399/140‑1 (MQ=255)
                                                                                                                                                  aCTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCAttt      >  5:167399/1‑140 (MQ=255)
                                                                                                                                                    |                                                                                                                                             
CCCGTCCATACCAGGCATGCGCGCATCGCTCATCACCAGATCAACCGGGCCCTCGGCCATCTGCGCCAGTGCCTGTTCGCCGCTGGTCGCCAGCTTCACGTCATAGGGTTGGCCACGCAATAGCCGACGCAGACTGCTAAGGATCGACTCCTCGTCGTCCACTAGCAACACGGTCGGCCGATAGGGTGGGTTCGGGTTCGGTTGCACTTCCATGGCAGGCCTCACGCGGTCGATCGATGGAGGCACTCGAGCTCAACGAGCGCTTAGGTCAAAGGCTAGATCATTTTTCC  >  NC_002947/3346287‑3346576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑