Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,041,300 T→A 8.9% intergenic (+230/‑432) PP_5680 → / → PP_4447 Cro/CI family transcriptional regulator/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,041,3000TA 8.9% 171.1 / 7.0 56intergenic (+230/‑432)PP_5680/PP_4447Cro/CI family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (25/26);  new base A (2/3);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

GTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGAAAAGTCATT  >  NC_002947/5041152‑5041444
                                                                                                                                                    |                                                                                                                                                
gtgtTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATg                                                                                                                                                 <  2:970923/150‑1 (MQ=255)
     gATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGGCCTCTTCAGCGGTGCGCCTTGAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGt                                                                                                                                            <  2:526382/150‑1 (MQ=255)
       tCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGttt                                                                                                                                          >  1:733763/1‑150 (MQ=255)
       tCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGtta                                                                                                                                          <  2:411553/150‑2 (MQ=255)
        ccACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTtc                                                                                                                                         <  1:225971/150‑1 (MQ=255)
                          aGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                                                                       <  2:1049696/150‑1 (MQ=255)
                              ttAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGa                                                                                                                   >  1:1059953/1‑150 (MQ=255)
                                            tCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGa                                                                                                     <  2:175501/150‑1 (MQ=255)
                                             cTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAg                                                                                                    <  1:1098463/150‑1 (MQ=255)
                                              tGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttag                                                                                                                                         <  2:621639/112‑3 (MQ=255)
                                              tGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttag                                                                                                                                         >  1:621639/1‑110 (MQ=255)
                                               gATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgctg                                                                                                                      >  2:1208666/1‑130 (MQ=255)
                                               gATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgctg                                                                                                                      <  1:1208666/130‑1 (MQ=255)
                                                   ccAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTccaac                                                                                              >  2:561373/1‑150 (MQ=255)
                                                    cAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTccaacc                                                                                             >  1:283484/1‑150 (MQ=255)
                                                      acacCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTccaaccaa                                                                                           >  1:1338061/1‑150 (MQ=255)
                                                          ctctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCt                                                                                       >  2:914465/1‑150 (MQ=255)
                                                            ctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGAAGAGGGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAt                                                                                     >  1:1142770/1‑150 (MQ=255)
                                                                        cATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTgg                                                                         >  2:1376428/1‑150 (MQ=255)
                                                                            aCCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTct                                                                                                                          >  1:254952/1‑97 (MQ=255)
                                                                            aCCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTct                                                                                                                          <  2:254952/97‑1 (MQ=255)
                                                                              ctctTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGAc                                                                   <  2:1059953/150‑1 (MQ=255)
                                                                               tctTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGAcc                                                                  >  2:1160586/1‑150 (MQ=255)
                                                                               tctTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttaggg                                                                                                                                       <  1:616280/81‑5 (MQ=38)
                                                                               tctTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttaggg                                                                                                                                       >  2:616280/1‑77 (MQ=38)
                                                                               gctTCATCGTCGCGCCTTAAGCCCGCCGAGCAGCGACAGAGACCCCGAGTAAGGCCCCTTCCCGTCTTATTGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGAcc                                                                  <  2:589960/149‑1 (MQ=255)
                                                                                    aTCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGt                                                             >  2:576236/1‑150 (MQ=255)
                                                                                          gcgcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCg                                                       >  1:44139/1‑150 (MQ=255)
                                                                                           cgcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgt                                                      <  2:283484/150‑1 (MQ=255)
                                                                                            gcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgtg                                                     <  2:733763/150‑1 (MQ=255)
                                                                                             ccTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgtgt                                                    <  2:44139/150‑1 (MQ=255)
                                                                                               ttAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGc                                                  <  1:576236/150‑1 (MQ=255)
                                                                                               ttAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGc                                                  <  1:914465/150‑1 (MQ=255)
                                                                                               ttAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGc                                                  >  1:372860/1‑150 (MQ=255)
                                                                                                             aagaGCCAGAGACCCCTAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGt                                    <  1:601388/150‑1 (MQ=255)
                                                                                                             aagaGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCa                                                                                                                              <  2:1207860/60‑1 (MQ=255)
                                                                                                             aagaGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCa                                                                                                                              >  1:1207860/1‑60 (MQ=255)
                                                                                                                   cAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGc                                                                                                               <  1:501691/69‑1 (MQ=255)
                                                                                                                   cAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGc                                                                                                               >  2:501691/1‑69 (MQ=255)
                                                                                                                          cccGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCa                       >  1:1306777/1‑150 (MQ=255)
                                                                                                                           ccGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTAGCAGAGAAAAGTGGTATCAATATCAg                      >  2:890064/1‑150 (MQ=255)
                                                                                                                               gCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGGTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGcccc                  <  2:1338061/150‑1 (MQ=255)
                                                                                                                                   gACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGc                                                        <  1:1260724/108‑1 (MQ=255)
                                                                                                                                   gACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGc                                                        >  2:1260724/1‑108 (MQ=255)
                                                                                                                                    aCCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCAcc             >  1:1390445/1‑150 (MQ=255)
                                                                                                                                      cccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAtt                                                                                    >  2:1026539/1‑77 (MQ=255)
                                                                                                                                      cccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAtt                                                                                    <  1:1026539/77‑1 (MQ=255)
                                                                                                                                      cccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCAGATTCCAAACAATTCTATTTTTCGACCTGGCCTTACCGCAGTAGAGCGTGTGCTATCAGAGAAACGTGGTATCAATCTCAGCCCCACACCgg           >  1:185729/1‑149 (MQ=255)
                                                                                                                                       ccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTg                                   >  2:458345/1‑125 (MQ=255)
                                                                                                                                       ccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTg                                   <  1:458345/125‑1 (MQ=255)
                                                                                                                                        cTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCa                                                               <  1:62417/96‑1 (MQ=255)
                                                                                                                                        cTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCa                                                               >  2:62417/1‑96 (MQ=255)
                                                                                                                                         tAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGaaaa        <  1:1160586/150‑1 (MQ=255)
                                                                                                                                             cGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCaga                                           <  1:817680/111‑1 (MQ=255)
                                                                                                                                             cGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCaga                                           >  2:817680/1‑111 (MQ=255)
                                                                                                                                               ccTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGAAAAGTCAtt  <  2:343492/150‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
GTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGAAAAGTCATT  >  NC_002947/5041152‑5041444

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: ‑