Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,020,511 T→A 12.2% L393* (TTG→TAG) ‡ PP_3546 → two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,020,5110TA12.2% 136.3 / 10.5 49L393* (TTG→TAG) ‡PP_3546two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (21/22);  new base A (3/3);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

CCTGGACCAGTCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTATGCATCAACGCGCGCGAT  >  NC_002947/4020365‑4020659
                                                                                                                                                  |                                                                                                                                                    
ccTGGACCAGTCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTtggt                                                                                                                                                   >  1:356505/1‑150 (MQ=255)
        aGTCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCa                                                                                                                                           <  1:362790/150‑1 (MQ=255)
         gTCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCAt                                                                                                                                          >  2:621670/1‑150 (MQ=255)
          tCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCAAGGTGGccac                                                                                                                                             >  1:120975/1‑144 (MQ=255)
          tCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCAAGGTGGccac                                                                                                                                             <  2:120975/146‑3 (MQ=255)
            aCGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCg                                                                                                                                              <  2:702007/143‑1 (MQ=255)
            aCGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCg                                                                                                                                              >  1:702007/1‑143 (MQ=255)
                ttCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGAc                                                                                                                                   <  2:445175/150‑1 (MQ=255)
                ttCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGAc                                                                                                                                   >  2:375671/1‑150 (MQ=255)
                ttCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGAc                                                                                                                                   <  2:356505/150‑1 (MQ=255)
                   gACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACctg                                                                                                                                <  1:372006/150‑1 (MQ=255)
                    aCGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCACCCCTGCTCCACGAAAGTGGCCACGTTGGTGGCCGGCATGGAAGACctgc                                                                                                                               <  1:739831/150‑1 (MQ=255)
                    aCGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCAAGGTGGcca                                                                                                                                              <  1:140340/135‑2 (MQ=255)
                    aCGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCAAGGTGGcca                                                                                                                                              >  2:140340/1‑134 (MQ=255)
                                  ttGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGTAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATc                                                                                                                 >  2:621139/1‑150 (MQ=255)
                                  ttGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTtggt                                                                                                                                                   >  2:714687/1‑116 (MQ=255)
                                  ttGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTtggt                                                                                                                                                   <  1:714687/116‑1 (MQ=255)
                                  ttGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATc                                                                                                                 >  1:669781/1‑150 (MQ=255)
                                   tGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCg                                                                                                                <  2:271363/150‑1 (MQ=255)
                                      tGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGGTCGAGCGCACCAGCGGcc                                                                                                             >  2:171771/1‑150 (MQ=255)
                                             gTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGAt                                                                                                      <  1:621670/150‑1 (MQ=255)
                                                 agcagcGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTAcc                                                                                                  <  2:412219/150‑1 (MQ=255)
                                                     caccggcgCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGa                                                                                              <  1:720705/147‑1 (MQ=255)
                                                                cGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCttt                                                                                   <  1:375671/150‑1 (MQ=255)
                                                                    ccTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGTAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTgcca                                                                               <  1:621139/150‑1 (MQ=255)
                                                                    ccTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTgcca                                                                               <  1:171771/150‑1 (MQ=255)
                                                                             tGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCCAGTAGCCACCTTGATATCGGGAGTGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCtgt                                                                      >  1:494928/1‑150 (MQ=255)
                                                                             tGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCtgt                                                                      >  2:633591/1‑150 (MQ=255)
                                                                               gTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTgg                                                                    <  1:66425/150‑1 (MQ=255)
                                                                                                gTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGAccc                                                   >  1:556257/1‑150 (MQ=255)
                                                                                                    tcCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTccc                                               <  2:556257/150‑1 (MQ=255)
                                                                                                      ccGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGa                                                                                              >  1:429692/1‑101 (MQ=255)
                                                                                                      ccGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGa                                                                                              <  2:429692/101‑1 (MQ=255)
                                                                                                                  ccTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCt                                                                                                <  2:662362/87‑1 (MQ=255)
                                                                                                                  ccTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAgcgc                                 >  2:493817/1‑150 (MQ=255)
                                                                                                                  ccTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGGGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCt                                                                                                >  1:662362/1‑87 (MQ=255)
                                                                                                                    tGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCt                               >  1:67421/1‑150 (MQ=255)
                                                                                                                          ccTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCa                         >  1:615173/1‑150 (MQ=255)
                                                                                                                          ccTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCa                         >  2:648036/1‑150 (MQ=255)
                                                                                                                                   cGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTATGCa                >  2:297997/1‑150 (MQ=255)
                                                                                                                                    gCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTATGCAt               >  2:645000/1‑150 (MQ=255)
                                                                                                                                         cggCCACCAAGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTAt                   <  2:90387/140‑1 (MQ=255)
                                                                                                                                         cggCCACCAAGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTAt                   >  1:90387/2‑141 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGc                                                                                                         >  1:285488/1‑52 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGc                                                                                                         <  2:285488/52‑1 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATc                                                        <  1:757600/101‑1 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATc                                                        >  2:757600/1‑101 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAgc                                   >  2:46732/1‑122 (MQ=255)
                                                                                                                                            ccACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAgc                                   <  1:46732/122‑1 (MQ=255)
                                                                                                                                             cACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTAt                   >  1:765935/1‑137 (MQ=255)
                                                                                                                                             cACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTAt                   <  2:765935/137‑1 (MQ=255)
                                                                                                                                             cACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTATGCATCAAcgcgcg      <  2:494928/150‑1 (MQ=255)
                                                                                                                                                 ttGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTGATGCATCAACGCGCGCGat  <  2:669781/150‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                    
CCTGGACCAGTCACGCTTCGACGCCCTGGCGCCCTTGCTGGAGCTGTCCAGCAGCGCGGCGCAGCGGGCCTCTTCGCTGGTGCACCGGCTGCTGGCGTTCTCCCGCCAGCAGACCCTGCAACCCTGCTCCACGCAAGTGGCCACCTTGGTGGCCGGCATGGAAGACCTGCTGCGCCGCACCATCGGCCCGGCGATTACCCTGAGCAGCCGCTTTGCCAGCCAGCTGTGGCCGACCTTCATCGACCCTCCCCAACTGGAAAGCGCCTTGCTCAACTTATGCATCAACGCGCGCGAT  >  NC_002947/4020365‑4020659

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑