Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	499,203	A→G	intergenic (+47/‑249)	uhpA → / → PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	499,203	0	A	G	100.0%	181.3 / NA	54	intergenic (+47/‑249)	uhpA/PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/29);  total (25/29)

AAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCG  >  NC_002947/499058‑499333                                                                                                                                                  |                                                                                                                                      aaGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg                                                                                                                                     >  1:49922/1‑148 (MQ=255)     ccATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGc                                                                                                                               >  1:295662/1‑149 (MQ=255)       aTCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGccc                                                                                                                             <  4:415003/149‑1 (MQ=255)       aTCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGccc                                                                                                                             <  7:326180/149‑1 (MQ=255)             aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGa                                                                                                                         >  7:31180/1‑147 (MQ=255)             aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑c                                                                                                                      <  1:31002/149‑1 (MQ=255)             aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑c                                                                                                                      <  7:172305/149‑1 (MQ=255)              cccACATGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑Cg                                                                                                                     <  4:132374/149‑1 (MQ=255)              cccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATTCCCGCGCA‑Cg                                                                                                                     >  6:240973/1‑149 (MQ=255)              cccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑Cg                                                                                                                     >  6:36677/1‑149 (MQ=255)               ccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑Cgg                                                                                                                    >  6:199301/1‑149 (MQ=255)                    aGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGggcctg                                                                                                               <  5:36677/149‑1 (MQ=255)                    aGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGGGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGggcctg                                                                                                               <  4:99833/149‑1 (MQ=255)                      gCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAAATGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGggcctggc                                                                                                             >  1:343533/1‑149 (MQ=255)                        aCGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CACGCCCGCGAA‑CGggccaggcct                                                                                                           >  8:151223/1‑149 (MQ=255)                        aCGCCTGATGCAGAAGTTGAAAGTGAAATCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGggcctggcct                                                                                                           >  1:227531/1‑149 (MQ=255)                         cGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGaa                                                                                                                        >  6:185630/1‑136 (MQ=255)                         cGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGaa                                                                                                                        <  5:185630/136‑1 (MQ=255)                            cTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCcggct                                                                                                        >  6:366991/1‑148 (MQ=255)                                   aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTa                                                                                                >  2:22322/1‑149 (MQ=255)                                     aaGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATg                                                                                              <  1:22322/149‑1 (MQ=255)                                        ttGAAATTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGTAGCGGG‑CATGCCCGCGAA‑CGggcctgg                                                                                                              >  2:314338/1‑130 (MQ=255)                                        ttGAAATTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGTAGCGGG‑CATGCCCGCGAA‑CGggcctgg                                                                                                              <  1:314338/130‑1 (MQ=255)                                            aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAg                                                                                        <  5:199301/148‑1 (MQ=255)                                              gTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGc                                                                                            >  6:139333/1‑142 (MQ=255)                                              gTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGc                                                                                            <  5:139333/142‑1 (MQ=255)                                              gTGAACTCCCTGGAGGAGCTGGTGAATTCAGCCATGCAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTATAAGAATACTATGTGCGCGCGGG‑CATGCCCGCGAA‑CGggcctggc                                                                                                             >  8:23464/1‑125 (MQ=255)                                                 aaCTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGc                                                                                   <  3:29752/148‑1 (MQ=255)                                                 aaCTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGc                                                                                   <  2:49922/148‑1 (MQ=255)                                                   cTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CAATCCCGCGAA‑CGGGCCTGGCCAGCTGATCTCTATGGCTGACCCCGccac                                                                                >  5:145368/1‑147 (MQ=255)                                                      gCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCtt                                                                             <  8:95580/148‑1 (MQ=255)                                                          gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTCATCTCTATGGCTGAGCCGGCC‑TCTTCGCgg                                                                        <  1:34692/149‑1 (MQ=255)                                                           cGGAGCTGGTGACGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGGGGGCGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCggg                                                                       <  3:118702/149‑1 (MQ=255)                                                               gCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCctgct                                                                                                        >  3:48474/1‑113 (MQ=255)                                                               gCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCctgct                                                                                                        <  4:48474/113‑1 (MQ=255)                                                                  ggTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGCGCCGGCC‑TCTTCGCGGGCATGccc                                                                >  5:208549/1‑149 (MQ=255)                                                                      aaGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCt                                                             <  2:227531/148‑1 (MQ=255)                                                                              cATGGAGCACACGCGGATCTGATTGCGACATAGGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGt                                                    <  6:208549/149‑1 (MQ=255)                                                                                 ggAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGCGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTc                                                 >  3:120719/1‑149 (MQ=255)                                                                                  gAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATTCCCGCGAA‑CGGGCCTGGGCAGCTGATCTCTATTGCTGAGCCGGCC‑TCTTAGCGGGCCTGCCCGCTCCCACAGGTTTCg                                                >  6:316518/1‑149 (MQ=255)                                                                                             gatctgatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATATCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCg                                     >  3:127339/1‑149 (MQ=255)                                                                                                  gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGGCTGCTGATCTCTATGGCTGAGCCGGGC‑TCTTCGCGGGCATGGCCGCTCCCCCAGGTTTGGTGGTTGGGTCGCAAgg                                >  3:127755/1‑149 (MQ=255)                                                                                                  gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCgg                                                                        <  7:362149/109‑1 (MQ=255)                                                                                                  gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCgg                                                                        >  8:362149/1‑109 (MQ=255)                                                                                                  gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCAGATCTATATGGCTGAGCCGGCC‑TCTTAGCGGGCATTCCCGCTCCCACACGTTTCGTGGTTGGCTAGCAAgg                                >  6:320787/1‑149 (MQ=255)                                                                                                   tttGCGACTTACGGGTCCCCTAAACTTGCCGATGCTTATGTGGGAGCGGG‑TATGCCGGCGAA‑GGGGCCTGGCGTGCTTTTCTCTTTGGCTGAGCGGGCC‑TCTTCGCGGGCTTGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAgg                                <  2:295662/147‑1 (MQ=25)                                                                                                   atTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATTCCCGCGAA‑CGGGCCTGGCCGGCTGATCTCTATGGCTGAGCCCGCC‑TCATCGCGGGCAAGCCCGCTCCCACAGGTTTCGTGGtt                                           >  2:29168/1‑137 (MQ=255)                                                                                                   atTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGtt                                           <  1:29168/137‑1 (MQ=255)                                                                                                   atTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGACTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCaa                                  <  7:85164/146‑1 (MQ=255)                                                                                                   atTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CACGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAgg                                <  7:151223/148‑1 (MQ=255)                                                                                                   atTGCCACATAGGGGTGCCCTAACCTGGCC‑TACCCTATTGGGGGCCGGGCCAGGCCGGCCAA‑CGGGCCGGGCCTGGTTATCTTTATGGCT‑CCCCGGCCGTTTTCGGGGGATGGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAgg                                <  2:343533/148‑1 (MQ=255)                                                                                                                     cctaaaCTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAAGCTCGCCGGGAGACCTATTCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCaa                       <  1:349467/137‑1 (MQ=25)                                                                                                                      cGAAACTTGCCGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGGTGGCAAGGGCCTTCCAATCCCGCCATcc            >  6:410275/1‑149 (MQ=255)                                                                                                                           cTTGCCGAAGCCTATGTGGGAGCGGG‑CAGGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCAGGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTa       <  5:316518/149‑1 (MQ=255)                                                                                                                                cGAAGCCTATGTGGGAGCGGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCg  <  5:320787/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                      AAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGG‑CATGCCCGCGAA‑CGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC‑TCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCG  >  NC_002947/499058‑499333

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑