Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,811,634 T→A 12.4% T262S (ACG→TCG)  PP_1615 ← LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,811,6340TA12.4% 139.3 / 8.9 55T262S (ACG→TCG) PP_1615LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (22/26);  new base A (4/3);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 6.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01

CCGCGAAGAGGCCAGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTGCAGCGCCAGTTAC  >  NC_002947/1811488‑1811780
                                                                                                                                                  |                                                                                                                                                   
ccGCGAAGAGGCCAGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTAt                                                                                                                                                   >  2:41075/1‑149 (MQ=255)
      agagGCCAGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTcggcg                                                                                                                                             <  6:106267/149‑1 (MQ=255)
        agGCCAGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGt                                                                                                                                           >  6:15962/1‑149 (MQ=255)
             aGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTg                                                                                                                                      >  8:44245/1‑149 (MQ=255)
              gTACCAGCAGCACCTCCCGTCAGCCGAACCGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCACCAACCGCCGAATACGGCGGtatgggc                                                                                                                                     <  7:71301/149‑7 (MQ=255)
                  cagcagCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACATGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTCCG‑CCt                                                                                                                                >  7:65946/1‑149 (MQ=255)
                  cagcagCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCt                                                                                                                                >  2:274406/1‑149 (MQ=255)
                  cagcagCACATCCCGTCAGCCG‑AACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACAGCCGAATTCGGCGGTTCGTGCG‑CCTc                                                                                                                               >  6:121126/1‑149 (MQ=255)
                         acaTCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCcagcag                                                                                                                         <  8:31228/149‑1 (MQ=255)
                          caTCCCGTCCGCCGAACCGATACGCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCtgcagc                                                                                                                        <  8:258418/149‑1 (MQ=255)
                          caTCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCagcagc                                                                                                                        <  7:88409/149‑1 (MQ=255)
                                    gCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGt                                                                                                                                       >  6:152075/1‑125 (MQ=255)
                                    gCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGt                                                                                                                                       <  5:152075/125‑1 (MQ=255)
                                       gAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAgcgccc                                                                                                           <  1:228761/149‑3 (MQ=255)
                                          aggATAGTCCGGCATCCCCGCCAACCCCTCCTTCAGGTAATCCAACAGCGGCAGTAGCTTCGGCGAGAGGTGCCTCTGCTTCTGATACAGCGCCCATACCGCGGTATTCGGCGGTTGGTGCG‑CCTGCAGCTGCGACACCAGCGcaccac                                                                                                        <  4:12207/147‑1 (MQ=255)
                                            gATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTg                                                                                                      >  5:70650/1‑149 (MQ=255)
                                                  ccGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGAATACGGCGGtatg                                                                                                                                        >  1:171890/1‑107 (MQ=255)
                                                  ccGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGAATACGGCGGtatg                                                                                                                                        >  1:89275/1‑107 (MQ=255)
                                                  ccGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGAATACGGCGGtatg                                                                                                                                        <  2:171890/110‑4 (MQ=255)
                                                  ccGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGAATACGGCGGtatg                                                                                                                                        <  2:89275/110‑4 (MQ=255)
                                                   cGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCGCCCTCCAGCAGCGACACCAGCGCACCACTGTTCAg                                                                                                 <  1:41075/148‑1 (MQ=255)
                                                        aCCCCTCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTcc                                                                                          <  5:121126/149‑1 (MQ=255)
                                                          cccGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAg                                                                                        >  6:247754/1‑149 (MQ=255)
                                                                     ctcctTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTc                                                                                                   <  8:146813/127‑1 (MQ=255)
                                                                     ctcctTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTc                                                                                                   <  8:5440/127‑1 (MQ=255)
                                                                     ctcctTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTc                                                                                                   >  7:5440/1‑127 (MQ=255)
                                                                     ctcctTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTc                                                                                                   >  7:146813/1‑127 (MQ=255)
                                                                     ctcctTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAAt                                                                             >  7:191571/1‑149 (MQ=255)
                                                                         ttCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGcac                                                                                                           <  2:150784/115‑1 (MQ=255)
                                                                         ttCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGcac                                                                                                           >  1:150784/1‑115 (MQ=255)
                                                                              gTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACt                                                                    >  8:257926/1‑149 (MQ=255)
                                                                               tAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTg                                                                   <  5:15962/149‑1 (MQ=255)
                                                                                   ccaccaGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGgtgt                                                                                             <  6:88967/119‑1 (MQ=255)
                                                                                   ccaccaGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGgtgt                                                                                             >  5:88967/1‑119 (MQ=255)
                                                                                      ccaGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAAc                                                            <  1:274406/149‑1 (MQ=255)
                                                                                           cgccgTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGAt                                                       <  7:44245/149‑1 (MQ=255)
                                                                                           cgccgTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGAt                                                       >  3:152056/1‑149 (MQ=255)
                                                                                            gccgTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGAtt                                                      <  3:106534/149‑1 (MQ=255)
                                                                                                tACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATACCtt                                                  <  5:247754/149‑1 (MQ=255)
                                                                                                aaggtacggcggCTGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCtt                                                  <  2:181798/143‑1 (MQ=255)
                                                                                                   cTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCa                                               <  7:257926/149‑1 (MQ=255)
                                                                                                   cTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCa                                               <  8:191571/149‑1 (MQ=255)
                                                                                                                   ctctGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTgg                                                                  <  8:314913/114‑1 (MQ=255)
                                                                                                                   ctctGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTgg                                                                  >  7:314913/1‑114 (MQ=255)
                                                                                                                        ctgcGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACgtagt                                                                                <  7:64080/95‑1 (MQ=255)
                                                                                                                        ctgcGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACgtagt                                                                                >  8:64080/1‑95 (MQ=255)
                                                                                                                          gcGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTACAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTgg                        >  8:148254/1‑149 (MQ=255)
                                                                                                                               tACAGCGCCCATACCGCCGTATTGGTCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCTCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATGCAGCACTGCCTGGCCAc                    <  8:65946/148‑1 (MQ=255)
                                                                                                                                  aGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGtt                >  7:271453/1‑149 (MQ=255)
                                                                                                                                   gcgcCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTg               >  4:257181/1‑149 (MQ=255)
                                                                                                                                     gcaccaaCCGCCGAATACGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGGTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTg               >  6:199961/7‑147 (MQ=255)
                                                                                                                                           aCCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTGCAgcgc         >  3:142531/1‑147 (MQ=255)
                                                                                                                                            ccgccgTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTGCAGCGCCAg      <  8:271453/149‑1 (MQ=255)
                                                                                                                                             cgccgTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACCTCCCGATTCCTTGCCGCGCCGCATCCAGCCCTGCCTGGCCAATGTTGCAGCGCCAGt     >  5:277205/1‑149 (MQ=255)
                                                                                                                                                cgTATTCGGCGGTTGGTGCG‑CCTCCAGCAGAGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTGCAGCGCCAGTTAc  <  6:70650/149‑1 (MQ=255)
                                                                                                                                                  tATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCg                                                                          <  3:45677/75‑1 (MQ=255)
                                                                                                                                                  tATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCg                                                                          >  4:45677/1‑75 (MQ=255)
                                                                                                                                                  |                                                                                                                                                   
CCGCGAAGAGGCCAGTACCAGCAGCACATCCCGTCAGCCGAAACGATACTCCGGCAACCCCGCCAACCCCTCCTTCAGGTAATCCACCAGCCGCCGTACCTTCGGCGACAGGTGCCTCTGCTGCGGATACAGCGCCCATACCGCCGTATTCGGCGGTTGGTGCG‑CCTCCAGCAGCGACACCAGCGCACCACTGTTCAGGTGTTCCAGCACGTAGTAATCCGGCAACTGGCACAACCCGATTCCTTGCAGCGCCGCATCCAGCACTGCCTGGCCACTGTTGCAGCGCCAGTTAC  >  NC_002947/1811488‑1811780

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: ‑