Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 888,986 G→A 7.4% R139H (CGC→CAC)  PP_0769 → sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947888,9860GA 7.4% 156.9 / 2.4 54R139H (CGC→CAC) PP_0769sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (22/28);  new base A (2/2);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.53e-01

ATCGAAGCTCAGCTGGCGGCGCACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCGG  >  NC_002947/888838‑889130
                                                                                                                                                    |                                                                                                                                                
aTCGAAGCTCAGCTGGCGGCGCACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCACTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCg                                                                                                                                                  >  6:61885/1‑149 (MQ=255)
       cTCAGCTGGCGGCGCACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGcc                                                                                                                                           >  7:71536/1‑149 (MQ=255)
               gcggcgCACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACg                                                                                                                                    <  8:316052/148‑1 (MQ=255)
                   cgcACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTg                                                                                                                               <  2:90488/149‑1 (MQ=255)
                         aGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGAt                                                                                                                          >  4:267151/1‑148 (MQ=255)
                         aGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCACTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATc                                                                                                                         <  5:61885/149‑1 (MQ=255)
                           gAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCAc                                                                                                                       >  5:127097/1‑149 (MQ=255)
                            aaGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCAcc                                                                                                                      <  8:71536/149‑1 (MQ=255)
                                  tCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCg                                                                                                                  >  4:249533/1‑147 (MQ=255)
                                    aaGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTg                                                                                                                                             >  4:204771/1‑118 (MQ=255)
                                    aaGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTg                                                                                                                                             <  3:204771/118‑1 (MQ=255)
                                    aaGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAaga                                                                                                              <  7:352954/149‑1 (MQ=255)
                                     aGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAG                                                                                                             >  5:92749‑M1/1‑149 (MQ=255)
                                       cacaACGACATTCTCGCCACTTGGCGCATCAACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACACGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGC                                                                                                           >  4:138280‑M1/1‑149 (MQ=255)
                                        acaACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCC                                                                                                          <  5:203289‑M1/149‑1 (MQ=255)
                                             gACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACaa                                                                                                     <  3:224624/149‑1 (MQ=255)
                                                aTTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCa                                                                                                  <  6:92749/149‑1 (MQ=255)
                                                    tcGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAAc                                                                                                    <  7:122501/143‑1 (MQ=255)
                                                    tcGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAAc                                                                                                    >  8:122501/1‑143 (MQ=255)
                                                      gCCACTTGGCTCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGTCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTgg                                                                                             <  5:190762/148‑1 (MQ=255)
                                                      gCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTgg                                                                                             <  6:220098/148‑1 (MQ=255)
                                                         aCTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCAt                                                                                         <  3:267151/149‑1 (MQ=255)
                                                              gcgcATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGc                                                                                     <  5:235292/148‑1 (MQ=255)
                                                                 cATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCt                                                                                                                             >  1:60368/1‑105 (MQ=255)
                                                                 cATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCt                                                                                                                             <  2:60368/105‑1 (MQ=255)
                                                                        acCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGa                                                                          >  2:74390/1‑149 (MQ=255)
                                                                            aCAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAg                                                                                                 >  1:202537/1‑122 (MQ=255)
                                                                            aCAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAg                                                                                                 <  2:202537/122‑1 (MQ=255)
                                                                             cAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGtcatcgttgacgcaaatggccaactggttgtcggcc                                                                     <  3:249533‑M1/149‑37 (MQ=255)
                                                                                           tcttcGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCaaa                                                        <  6:127097/148‑1 (MQ=255)
                                                                                             ttcGACCGCGAACTGGTGGCCTCTGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATc                                                            >  2:165847/1‑142 (MQ=255)
                                                                                             ttcGACCGCGAACTGGTGGCCTCTGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATc                                                            <  1:165847/142‑1 (MQ=255)
                                                                                             ttcGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGca                                                     >  4:313262/1‑149 (MQ=255)
                                                                                                     cgAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCACTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGC                                                                                                           <  1:146085‑M1/87‑1 (MQ=255)
                                                                                                     cgAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCACTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGC                                                                                                           <  1:140905‑M1/87‑1 (MQ=255)
                                                                                                     cgAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCACTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGC                                                                                                           >  2:140905‑M1/1‑87 (MQ=255)
                                                                                                     cgAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCACTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGC                                                                                                           >  2:146085‑M1/1‑87 (MQ=255)
                                                                                                      gAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTc                                              >  7:297012/1‑147 (MQ=255)
                                                                                                      gAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGa                                            <  3:138280/149‑1 (MQ=255)
                                                                                                       aaCTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAg                                           <  3:313262/149‑1 (MQ=255)
                                                                                                               gCCTCGGTGATCGCCAACGTCATCAACAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGTCCATTTGCGTAAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCagga                                   <  7:335872/149‑1 (MQ=255)
                                                                                                                ccTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCCACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCaggag                                  >  8:355039/1‑149 (MQ=255)
                                                                                                                 cTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCTGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATTACGGCCCggg                                                                 >  7:257634/1‑117 (MQ=255)
                                                                                                                 cTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCAt                                                                                         >  2:326483/1‑93 (MQ=255)
                                                                                                                 cTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCggg                                                                 <  8:257634/117‑1 (MQ=255)
                                                                                                                     gTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTa                             <  8:154647/149‑1 (MQ=255)
                                                                                                                           gCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATcc                        <  7:355039/148‑1 (MQ=255)
                                                                                                                           gCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCa                       <  8:297012/149‑1 (MQ=255)
                                                                                                                                        ccAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCggg                                                                 <  7:202634/94‑1 (MQ=255)
                                                                                                                                        ccAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCggg                                                                 >  8:202634/1‑94 (MQ=255)
                                                                                                                                          aaCGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCAGGGCAtcgactcgac        >  4:56666/1‑149 (MQ=255)
                                                                                                                                               cACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGtcatcgttgacgcaaatggccaactggttgtcggcctctt                                                                 <  4:58976‑M1/87‑41 (MQ=255)
                                                                                                                                               cACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGtcatcgttgacgcaaatggccaactggttgtcggcctctt                                                                 >  3:58976‑M1/1‑47 (MQ=255)
                                                                                                                                                aCCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCgg  >  4:170393/1‑149 (MQ=255)
                                                                                                                                                  ccGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCgg  >  2:301828/1‑147 (MQ=255)
                                                                                                                                                    gCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCGCATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCgg  <  2:6727/145‑1 (MQ=255)
                                                                                                                                                    gCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCGCATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCgg  >  1:6727/1‑145 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
ATCGAAGCTCAGCTGGCGGCGCACGAGGAAGTACTCAAGCACAACGACATTCTCGCCACTTGGCGCATCGACACCGACAACCCGCTGGGTTTCTTCGACCGCGAACTGGTGGCCTCGGTGATCGCCAACGTCATCACCAACGCCACCCGCTTTGCCGGGCACGCCTTGCTGATCACCATCGAAGAGGCCGACAACCAGTTGGCCATTTGCGTCAACGATGACGGCCCGGGTTATCCAAAGCACATGCTCGAGCGCCAGGAGGATTACATCCAGGGCATCGACTCGACCAGCGG  >  NC_002947/888838‑889130

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: ‑