Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	499,203	A→G	100%	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%	179.7 / NA	52	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 (24/28);  total (24/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑AGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAACA  >  NC_002947/499060‑499345                                                                                                                                                 |                                                                                                                                                gACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCAt                                                                                                                                            >  2:26922/1‑149 (MQ=255)   ccATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑c                                                                                                                                         <  3:175294/149‑1 (MQ=255)        aGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCcgc                                                                                                                                     <  7:220034/148‑1 (MQ=255)           aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGGGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAACCCTATGTGGGAGC‑GGGCATG‑CCCGCGAAc                                                                                                                                 <  3:47475/149‑1 (MQ=255)            cccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑‑CCGCGAACgg                                                                                                                               <  4:324085/149‑1 (MQ=255)             ccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACgg                                                                                                                               <  1:26922/149‑1 (MQ=255)             ccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACgg                                                                                                                               <  5:129664/149‑1 (MQ=255)             ccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACgg                                                                                                                               >  6:129664/1‑149 (MQ=255)              cacaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACggg                                                                                                                              >  7:270869/1‑149 (MQ=255)               acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGggc                                                                                                                             >  6:373717/1‑149 (MQ=255)                caAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGggcc                                                                                                                            >  8:121393/1‑149 (MQ=255)                  aGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGggcctg                                                                                                                          <  3:134132/149‑1 (MQ=255)                   ggCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGAACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGggcctgg                                                                                                                         >  5:171031/1‑149 (MQ=255)                    gCACGCCTCATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTCCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGggcctggc                                                                                                                        <  7:345270/149‑1 (MQ=255)                        gCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCctgc                                                                                                                    <  8:53758/149‑1 (MQ=255)                         ccTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCctgct                                                                                                                   <  7:261309/149‑1 (MQ=255)                          cTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGTAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCctgctg                                                                                                                  <  3:75131/149‑1 (MQ=255)                          cTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGGAATG‑CCC‑CGAACCGGCCGGGGctggtg                                                                                                                  >  3:10791/1‑149 (MQ=255)                           tGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGa                                                                                                                 >  1:272357/1‑149 (MQ=255)                             aTGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGAt                                                                                                                <  4:32513/148‑1 (MQ=255)                              tGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGAtct                                                                                                              <  7:142419/149‑1 (MQ=255)                                cAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGAtctc                                                                                                             <  2:188370/148‑1 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCcgc                                                                                                                                     >  2:63654/1‑123 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCcgc                                                                                                                                     <  1:63654/123‑1 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTa                                                                                                           <  2:272357/149‑1 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCAAT‑CCCGCGAACCGGCCTGGCCTGCTGCTCTCTa                                                                                                           >  3:213067/1‑149 (MQ=255)                                 aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGAGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCCTT‑GCCGCGCACCGGCCTGGCCTGCAGCtctcga                                                                                                           >  7:343350/1‑147 (MQ=255)                                       tGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                      <  7:121393/148‑1 (MQ=255)                                          aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATg                                                                                                         >  2:35257/1‑142 (MQ=255)                                          aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATg                                                                                                         <  1:35257/142‑1 (MQ=255)                                                        gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGGGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                    <  4:223634/149‑1 (MQ=255)                                                        gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                    <  8:270869/149‑1 (MQ=255)                                                        gCGGAGCTGGTGAAGAACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTcgc                                                                                      <  6:171031/147‑1 (MQ=255)                                                          ggAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGc                                                                                  <  2:336097/149‑1 (MQ=255)                                                                  tGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGGCTGGCCTGGTGCTGTCTATGGGTGGGCCCGCCGCTTCGCGGGCATGCCCGc                                                                          >  8:253839/1‑149 (MQ=255)                                                                      gTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTcc                                                                       >  2:63627/1‑148 (MQ=255)                                                                       tACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGGCTGCTGATCGCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCca                                                                     >  6:82351/1‑149 (MQ=255)                                                                           ccATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGGCTGCCCCCCGAACGGG‑CGGGGCGGGGGATAGGTATTGGTGAGCCGGCCGCTTGGCGGGCCTTCCCCCTGCcccacg                                                                 >  7:49870/1‑147 (MQ=255)                                                                              tGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCGGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGttt                                                              >  6:75184/1‑149 (MQ=255)                                                                                 aGCACATCCTGTTCTGATGGCCAAATACGGTTGCCCGAAACTTGCCTACGCATTTGGGGGCGC‑GGGCTTG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTTTGGCTGCGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGt                                                           <  8:273889/149‑1 (MQ=25)                                                                                   cacaAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTgg                                                         >  1:238182/1‑149 (MQ=255)                                                                                          tgatctgatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCACCCACAGGTTTCGTGGTTGGCTc                                                  >  1:49305/1‑149 (MQ=255)                                                                                            atctgatTCCGACATACGGGTGCCCGAAACTTGCCTCAGCCTTGGTGGGCGC‑GGGCATG‑CCCGCGAACGGGCGTGGCCTGCTTATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCg                                                 <  4:213067/148‑1 (MQ=38)                                                                                                gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                    <  7:68920/109‑1 (MQ=255)                                                                                                gatTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                    >  8:68920/1‑109 (MQ=255)                                                                                                     ccaCATTCGGGTGCCCCAAACTTCCCTACCCTTTTGTGGCTGG‑GGGCTGG‑CCCGCTACGGGGCCTGGCCGGCTTATCTCTATGGCTGAGCCGGCCTCTTCGGGGGATTGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCAtt                                       <  4:342928/147‑1 (MQ=255)                                                                                                                   ccGAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATc                         >  5:191695/1‑149 (MQ=255)                                                                                                                     gAAACTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCt                       <  1:63627/149‑1 (MQ=255)                                                                                                                         cTTGCCGAAGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTa                   <  2:238182/149‑1 (MQ=255)                                                                                                                                aaGCCTATGTGGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCGGCTGATCTCTATGGGTGAGCCGGCCGCTTAGCGGGTATGCCCGCGCCCACAGGGTTGGGGGTTGACTCGCAAGGGCATTGACATACCGCCAAACATGTAGTGCGa             >  6:227639/1‑148 (MQ=255)                                                                                                                                        gtgGGAGC‑GGGCATG‑CCCGCGAACGGGCCTGGGCTGGTGATGTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGGGGTTGGGTCGGAAGGGGCTTGCAATACCGCCATCCTTGTAGGGGGGTCCCTacaa    >  6:178392/1‑149 (MQ=37)                                                                                                                                           ggAGC‑GGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATGGCTATGGCTGAGCCGGCCGCTTAGCGGGCATGCCCGCTCCCACAGGTTTCGGGGTTGGGTCGCCAGGGCATTGCAATGCCGCCATCCTTGTAGGGCGATCCCTaaaaca  >  2:237184/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                GACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGC‑AGGCATG‑CCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAACA  >  NC_002947/499060‑499345

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: ‑