Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 317,974 Δ1 bp 7.7% coding (1768/1815 nt) PP_0264 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947317,9740C. 7.7% 158.3 / 7.4 52coding (1768/1815 nt)PP_0264sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base C (25/22);  new base . (2/2);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

AGCCCGGCCAGGTCCAGGGTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTGAAGAACGGCTC  >  NC_002947/317827‑318121
                                                                                                                                                   |                                                                                                                                                   
aGCCCGGCCAGGTCCAGGGTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGc                                                                                                                                                     <  7:101873/148‑1 (MQ=255)
      gCCAGGTCCAGGGGCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGc                                                                                                                                              <  3:229483/149‑1 (MQ=255)
               aGGGTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGgaga                                                                                                                                     <  5:76160/149‑1 (MQ=255)
               aGGGTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGgaga                                                                                                                                     <  8:138726/149‑1 (MQ=255)
                gggTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGagag                                                                                                                                    >  7:87756/1‑149 (MQ=255)
                       gCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCAATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAg                                                                                                                                <  4:39494/146‑1 (MQ=255)
                        cTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGACGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGTGAGGCAGCAtt                                                                                                                            >  8:89359/1‑149 (MQ=255)
                           aaGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTgcg                                                                                                                         >  2:145750/1‑149 (MQ=255)
                              gCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCa                                                                                                                      <  2:19287/149‑1 (MQ=255)
                                            ggggTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGTGTTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCGGGAGAGTCCGCATTGCGCCACCTTCCGggtgggt                                                                                                        >  8:333931/1‑147 (MQ=255)
                                             gggTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCGACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTg                                                                                                       >  7:4429/1‑149 (MQ=255)
                                                  aTCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGAGGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCcag                                                                                                  <  7:89359/149‑1 (MQ=255)
                                                    cGTCCACCAGGATCACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGTCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCcagca                                                                                                <  5:11432/149‑1 (MQ=255)
                                                     gTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCcagcag                                                                                               <  8:4429/149‑1 (MQ=255)
                                                          ccaGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGtt                                                                                          >  5:209069/1‑149 (MQ=255)
                                                                         cTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGgcgc                                                                           <  6:209069/149‑1 (MQ=255)
                                                                                   gATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCcagc                                                                                                 <  6:62123/117‑1 (MQ=255)
                                                                                   gATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCcagc                                                                                                 >  5:62123/1‑117 (MQ=255)
                                                                                       aGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTca                                                             >  1:340128/1‑149 (MQ=255)
                                                                                        gtgtCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTcac                                                            <  1:145750/149‑1 (MQ=255)
                                                                                           tctcGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCa                                                                                 >  4:190262/1‑125 (MQ=255)
                                                                                           tctcGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCa                                                                                 <  3:190262/125‑1 (MQ=255)
                                                                                               ggtggtCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATg                                                       <  6:123990/147‑1 (MQ=255)
                                                                                               ggtggtCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATg                                                       <  8:168895/147‑1 (MQ=255)
                                                                                               ggtggtCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGc                                                     <  2:340128/149‑1 (MQ=255)
                                                                                                   gtCATGCCGTGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGc                                                 <  8:225250/149‑1 (MQ=255)
                                                                                                   gtCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCGCCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGc                                                 >  8:273347/1‑149 (MQ=255)
                                                                                                      aTGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCa                                                                     >  8:311983/1‑126 (MQ=255)
                                                                                                      aTGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCa                                                                     <  7:311983/126‑1 (MQ=255)
                                                                                                        gCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCcccag                                            >  3:76983/1‑149 (MQ=255)
                                                                                                          cGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATCCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCcccaggc                                          >  4:156383/1‑149 (MQ=255)
                                                                                                           gAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCcccaggcc                                         >  6:273988/1‑149 (MQ=255)
                                                                                                              gggTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCcccaggcccag                                      <  8:87756/149‑1 (MQ=255)
                                                                                                                   ctccGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCt                                 >  3:174261/1‑149 (MQ=255)
                                                                                                                   ctccGAATTGGGCAAAGTAGCGCCAGATGCGG‑CACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTc                                                              >  4:275672/1‑119 (MQ=255)
                                                                                                                   ctccGAATTGGGCAAAGTAGCGCCAGATGCGG‑CACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTc                                                              >  4:270816/1‑119 (MQ=255)
                                                                                                                   ctccGAATTGGGCAAAGTAGCGCCAGATGCGG‑CACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTc                                                              <  3:270816/119‑1 (MQ=255)
                                                                                                                   ctccGAATTGGGCAAAGTAGCGCCAGATGCGG‑CACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTc                                                              <  3:275672/119‑1 (MQ=255)
                                                                                                                     ccGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTgg                               >  7:60716/1‑149 (MQ=255)
                                                                                                                     ccGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTgg                               >  6:6809/1‑149 (MQ=255)
                                                                                                                      cGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGtt                                                                                                        >  7:2928/1‑75 (MQ=255)
                                                                                                                      cGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGtt                                                                                                        <  8:2928/75‑1 (MQ=255)
                                                                                                                         aTTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGc                           <  5:273988/149‑1 (MQ=255)
                                                                                                                              gCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTc                      >  2:338754/1‑149 (MQ=255)
                                                                                                                                    tAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTtggtg                <  7:333931/149‑1 (MQ=255)
                                                                                                                                        gcCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGcc                                                >  8:101005/1‑113 (MQ=255)
                                                                                                                                        gcCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGcc                                                <  7:101005/113‑1 (MQ=255)
                                                                                                                                         ccAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTgaa           >  7:86255/1‑149 (MQ=255)
                                                                                                                                           aGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTgaag          >  5:62617/1‑148 (MQ=255)
                                                                                                                                             aTGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCAAGGGCGCGCATCAGGCTTTCACACGTGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTGAAGAAc       >  7:193656/1‑149 (MQ=255)
                                                                                                                                               gCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTGAAGAACgg     >  1:92331/1‑149 (MQ=255)
                                                                                                                                                cGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTGAAGAACgg     <  4:76983/148‑1 (MQ=255)
                                                                                                                                                  gCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCGGGGTGCGGGTCTTGGTGGTGAAGAACGGCTc  >  2:317746/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                   
AGCCCGGCCAGGTCCAGGGTCTGGCTCAAGGCTTGGCGCAGGTGGGGGTCATCGTCCACCAGGATGACCTGGGCTCGGCTGTCGATCAGTGTCTCGGTGGTCATGCCGAGGGGTCCTCCGAATTGGGCAAAGTAGCGCCAGATGCGGCCACCCGCAGCTGGAGAGTCAGCATTGCGCCACCTTCCGGGTGGTTGGCCAGCAGCAGTTCACCGCCCAGGGCGCGCATCAGGCTTTCACAGATGGCCAGCCCCAGGCCCAGGCCCTGGGTGCGGGTCTTGGTGGTGAAGAACGGCTC  >  NC_002947/317827‑318121

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: ‑