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%	180.4 / NA	55	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 (28/27);  total (28/27)

GACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAA  >  NC_002947/499060‑499343                                                                                                                                                 |                                                                                                                                             gACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCAt                                                                                                                                         >  8:328279/1‑149 (MQ=255)  aCCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGAGGGAGCGGGCATg                                                                                                                                        >  8:383293/1‑149 (MQ=255)    cATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGcc                                                                                                                                      >  6:318651/1‑149 (MQ=255)      tCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATTCCcg                                                                                                                                    >  1:334926/1‑149 (MQ=255)          cACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGc                                                                                                                                           >  4:375839/1‑138 (MQ=255)          cACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGc                                                                                                                                           <  3:375839/138‑1 (MQ=255)             ccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACGAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACgg                                                                                                                             >  8:282578/1‑149 (MQ=255)               acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAATCTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGggc                                                                                                                           <  6:112922/149‑1 (MQ=255)                        gCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTACTGTGGGAGCGGGCATGCCCGCGAACGGgcctggcctg                                                                                                                   <  1:74952/149‑1 (MQ=255)                         ccTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGggc                                                                                                                           <  5:327674/139‑1 (MQ=255)                         ccTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGggc                                                                                                                           >  6:327674/1‑139 (MQ=255)                          cTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCctgctg                                                                                                                <  7:383293/149‑1 (MQ=255)                              tGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACGAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGAtct                                                                                                            <  7:282578/149‑1 (MQ=255)                                 aGATGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTa                                                                                                         <  8:178326/149‑1 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATCGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCAATCCCCCCAACCGGCCTGACCAGCTGAtctat                                                                                                          >  5:171307/1‑146 (MQ=255)                                       tGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGTGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTa                                                                                                         >  3:308923/1‑143 (MQ=255)                                       tGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGTGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTa                                                                                                         <  4:308923/143‑1 (MQ=255)                                       tGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCAGGCCTGCTGATCTCTATGGCt                                                                                                    >  1:77828/1‑148 (MQ=255)                                          aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGc                                                                                                <  3:317129/149‑1 (MQ=255)                                          aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCGGGCCTGCTGATCTCTATGGCTGAGc                                                                                                >  2:317229/1‑149 (MQ=255)                                           aGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgg                                                                                                      >  7:106471/1‑142 (MQ=255)                                           aGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgg                                                                                                      <  8:106471/142‑1 (MQ=255)                                           aGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGa                                                                                                  >  6:380171/1‑146 (MQ=255)                                           aGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGa                                                                                                  <  5:380171/146‑1 (MQ=255)                                           aGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGcc                                                                                               >  5:231922/1‑149 (MQ=255)                                               aaCTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGcc                                                                                           >  5:410279/1‑149 (MQ=255)                                               aaCTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGcc                                                                                           >  6:195255/1‑149 (MQ=255)                                                    gCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACTAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGTGCAGGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                    <  2:55991/135‑1 (MQ=255)                                                    gCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                    >  1:55991/1‑135 (MQ=255)                                                    gCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCtt                                                                                       <  6:410279/148‑1 (MQ=255)                                                        gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGCTCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTcgc                                                                                    <  5:195255/147‑1 (MQ=255)                                                        gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                  <  6:231922/149‑1 (MQ=255)                                                                 gTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGACTCTTCGCGGGCATGcc                                                                           <  5:318651/147‑1 (MQ=255)                                                                      ttACGCCATGTATCACAAGCTTATCTTATTGCGACATACGGGTGCCCGAAACTTGCCTACGCATA‑TGTGGGAGCGGGCATGCCCGCTAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTcc                                                                     <  6:201337/147‑1 (MQ=255)                                                                      gTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTcc                                                                     >  3:273867/1‑148 (MQ=255)                                                                      gTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATATATATGGCTGAGCCGGCCTCTTAGCGGGCATGCCCGCTcc                                                                     >  5:201337/1‑148 (MQ=255)                                                                       tACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                    >  3:244138/1‑116 (MQ=255)                                                                       tACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                    <  4:244138/116‑1 (MQ=255)                                                                          gCCTTGGAGCACAAGCTTATCTGATTGCGAAATACGGGTGCCCGAAACTTGCCTATGCCTT‑TGTGGGAGGGGGCTTGCCCGCTAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTGGCGGGCATGCCCGCTCCCACAg                                                                <  2:77828/149‑1 (MQ=38)                                                                          gCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgg                                                                                                      >  6:369107/1‑111 (MQ=255)                                                                            cATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCCCCAACGGGCCTTGGCTGAAGATCAATATTGCTGAACCGGCCTCATACCCGGCAAGCCCGCTCCCACACGt                                                              >  8:25863/1‑149 (MQ=255)                                                                                        gCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATATCTATGGCTGAGCCGGCCTCTTAGCGGGCATGCCCGCTccc                                                                    >  1:22266/1‑131 (MQ=255)                                                                                         ctgttctgttTGCGCCTTCGGGGGGCCCTAAAGTTCCCGAGGCGTT‑TGGGGGTGGGGGCAGGCCCGCTACGGGGCCTGGCGTGCTGATCTCTTGGGCTGCGCGGGCCTCTTCGCGGGATTGCCCGCTCCCACAGGTTTCGTGGTTGGc                                                  <  2:334926/148‑1 (MQ=255)                                                                                              ctgatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCgg                                                                                             >  2:387271/1‑100 (MQ=255)                                                                                               tgatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCCTGGCCGCGAACGGGCCGGGCCGGGGGGTCTGTATTGCTGGGGCCGCCTCGTAGCGGGGCTGGCCCCGCCCCCAGGTTTGGTGGTTTGGTGGCaac                                           >  8:354228/1‑148 (MQ=255)                                                                                                 atTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCaa                                            <  4:273867/146‑1 (MQ=255)                                                                                                  ttGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCGGCTGATCGCTATGGCTGCGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAggg                                         >  5:101702/1‑148 (MQ=255)                                                                                                                    ctaacattGCCGAAGCCTA‑TGGGGGAGCGGGCATGCCCGCGAAGGGGCCTGGCCTGCTGATCTATATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATcc                      <  3:234317/143‑1 (MQ=38)                                                                                                                     gAAACTTGCCGAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTAGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCAACCt                     >  6:204319/1‑149 (MQ=255)                                                                                                                        aCTGGCCGACGCCTA‑GGGGGGCGCGGCCATGCCCGCGAACGGGCCTGGCCGGCTCAGCTCAATGGCGCAGCCGCCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGt                  <  5:339300/149‑1 (MQ=37)                                                                                                                         ctgcccGAAGCCTT‑GGGGGCAGCGGCCTTGCCCGCGACGGGGCCGGGCCTGCTTATCTCTATGGCTGCCCCGGCCTCTGCGCGGGCAGGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTa                 <  7:354228/145‑1 (MQ=255)                                                                                                                               gAAGCCTA‑TGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGa           >  2:71557/1‑149 (MQ=255)                                                                                                                                 acccTA‑TGTGGGAGCGGGCATGCCCGCTAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATc         <  7:25863/147‑1 (MQ=255)                                                                                                                                          tgGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGATCGCCCTacaa  <  1:317229/148‑1 (MQ=39)                                                                                                                                          ggggAGGGGGCATGCCCGCGAACGGGCCGGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCTTGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGATCGCCCTacaa  <  7:328279/147‑1 (MQ=38)                                                                                                                                                 |                                                                                                                                             GACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTA‑TGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAA  >  NC_002947/499060‑499343

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: ‑