Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,486,759	T→A	6.9%	L14M (TTG→ATG) ‡	PP_4824 →	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_002947	5,486,759	0	T	A	6.9%	178.9 / 4.6	58	L14M (TTG→ATG) ‡	PP_4824	two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (24/30);  new base A (2/2);  total (26/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GCGGCATCCGGCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGCCGACC  >  NC_002947/5486617‑5486906                                                                                                                                                  |                                                                                                                                                    gCGGCATCCGGCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCTCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGAc                                                                                                                                              <  1:1029023/150‑1 (MQ=255)  cGGCATCCGGCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGAcc                                                                                                                                             <  2:436257/150‑1 (MQ=255)      aTCCGGCTCGTCGACAGGGCCCGGCATGGGCCTTGCCTTCGACTTTGCGCGCCGCGCCTAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTAAGCTTGCTGACCCTGc                                                                                                                                         >  2:1314469/1‑150 (MQ=255)         cGGCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGctct                                                                                                                                      <  2:896820/150‑1 (MQ=255)           gCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGc                                                                                                                                    >  2:247115/1‑150 (MQ=255)            cTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCa                                                                                                                                   <  1:863974/150‑1 (MQ=255)            cTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCa                                                                                                                                   <  1:1205288/150‑1 (MQ=255)                  aaCAGGGCCCAGAATGTGCGTTGCCCTCGACGTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTc                                                                                                                             <  2:553834/149‑1 (MQ=255)                            ggAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGc                                                                                                                   >  1:1094659/1‑150 (MQ=255)                                     cttgccttCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGa                                                                                                          <  1:701612/150‑1 (MQ=255)                                              gACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGc                                                                                                                                    <  2:112143/115‑1 (MQ=255)                                              gACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGc                                                                                                                                    >  1:112143/1‑115 (MQ=255)                                              gACTTGGCGCGCCGCGCATAGTGAGTACACGGCACCATGGATCCTAGTAATGGACT‑‑G‑AGTGCTTCTGCTTCGCAATGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTg                                                                                                 <  1:673719/150‑1 (MQ=255)                                                cTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTGGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGa                                                                                               <  1:351704/150‑1 (MQ=255)                                                      gcgccgcgcATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCAAGCTGAc                                                                                                                                              <  1:1418357/97‑1 (MQ=255)                                                      gcgccgcgcATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCAAGCTGAc                                                                                                                                              >  2:1418357/1‑97 (MQ=255)                                                                    gAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAg                                                                           >  1:505632/1‑150 (MQ=255)                                                                     aGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCCGCTTCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAgg                                                                          <  2:201008/150‑1 (MQ=255)                                                                          ccGGCA‑CATCG‑GCCCAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTTGACCGTTCTGCTCCACGAGCACGCCAAc                                                                     >  2:206194/1‑150 (MQ=255)                                                                          ccGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCAGGCTGCGGCCGAACATGACGGTGGCTGGACCg                                                                                            <  2:382541/127‑1 (MQ=255)                                                                          ccGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCAGGCTGCGGCCGAACATGACGGTGGCTGGACCg                                                                                            >  1:382541/1‑127 (MQ=255)                                                                                         cAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCg                                                        >  2:105136/1‑150 (MQ=255)                                                                                          aag‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTTAGCGa                                                       >  2:537375/1‑150 (MQ=255)                                                                                          aag‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGa                                                           <  1:303575/146‑1 (MQ=255)                                                                                          aag‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGa                                                           >  2:303575/1‑146 (MQ=255)                                                                                          aag‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGa                                                       >  2:966190/1‑150 (MQ=255)                                                                                            g‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGAtg                                                     >  1:315305/1‑150 (MQ=255)                                                                                            g‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCAAGCTGAc                                                                                                                                              <  1:193424/61‑1 (MQ=255)                                                                                            g‑aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCAAGCTGAc                                                                                                                                              >  2:193424/1‑61 (MQ=255)                                                                                              aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGAtgt                                                    <  2:120361/150‑1 (MQ=255)                                                                                              aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGAtgt                                                    >  1:632809/1‑150 (MQ=255)                                                                                              aagGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCCGCTGTTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGAtgt                                                    <  1:247115/150‑1 (MQ=255)                                                                                               agGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGAtgtg                                                   >  1:248620/1‑150 (MQ=255)                                                                                                       ttttgTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGAAGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGa                                           <  1:206194/146‑1 (MQ=255)                                                                                                        gTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAg                                          >  2:1309622/1‑150 (MQ=255)                                                                                                           gTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGAcc                                                                                             >  1:787224/1‑96 (MQ=255)                                                                                                           gTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGAcc                                                                                             <  2:787224/96‑1 (MQ=255)                                                                                                               gTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAg                                                          >  1:1378222/1‑127 (MQ=255)                                                                                                               gTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAg                                                          <  2:1378222/127‑1 (MQ=255)                                                                                                                   gCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCaa                               <  1:721580/150‑1 (MQ=255)                                                                                                                    cTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAAc                              <  1:1239824/150‑1 (MQ=255)                                                                                                                        ggATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGAc                                                                                              <  2:893363/82‑1 (MQ=255)                                                                                                                        ggATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGAc                                                                                              >  1:893363/1‑82 (MQ=255)                                                                                                                           ttGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCa                       <  2:315305/150‑1 (MQ=255)                                                                                                                            tGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAg                      <  2:632809/150‑1 (MQ=255)                                                                                                                             gCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGc                     <  2:248620/150‑1 (MQ=255)                                                                                                                                tCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGc                     <  2:128980/147‑1 (MQ=255)                                                                                                                                tCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGc                     >  1:128980/1‑147 (MQ=255)                                                                                                                                tCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCa                  <  1:1309622/150‑1 (MQ=255)                                                                                                                                             tCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAgg                                                                          >  1:93920/1‑81 (MQ=255)                                                                                                                                             tCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAgg                                                                          <  2:93920/81‑1 (MQ=255)                                                                                                                                             tCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGCCg     >  2:1145505/1‑150 (MQ=255)                                                                                                                                               aGCTTGCTGGCCCTGCTCTGCATGTTTCCGGCTGCCGCCCAACATGACGGTGGCTGCACCGTTCTGCAAGTCGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGCCGAc   <  1:1314469/150‑1 (MQ=255)                                                                                                                                               aGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGcc      >  2:400152/1‑147 (MQ=255)                                                                                                                                               aGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGcc      <  1:400152/147‑1 (MQ=255)                                                                                                                                                gCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCa                            <  2:861472/124‑1 (MQ=255)                                                                                                                                                gCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCa                            >  1:861472/1‑124 (MQ=255)                                                                                                                                                gCTTGCTAACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCGCGCCGAcc  >  1:713476/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                    GCGGCATCCGGCTCGTCGACAGGGCCCGGAATGGGCCTTGCCTTCGACTTGGCGCGCCGCGCATAGTGAGTACCCGGCA‑CATCG‑GCCAAG‑AAGGGATTTCGTAGTGCGTCGGCTTCGGATTGCCTCAGCTCTGATCGTCAGCTTGCTGACCCTGCTCTGCATGTTTCCGGCTGCGGCCGAACATGACGGTGGCTGGACCGTTCTGCTCGACGAACAGGCCAACCTGCAACTGAGCGATGTGCGCTCCGAGCGCTATCGCAACCAGTTCAGCCCACTGCCTCTCGCCGACC  >  NC_002947/5486617‑5486906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑