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%	172.2 / NA	51	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 (26/25);  total (26/25)

CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAAC  >  NC_002947/499057‑499344                                                                                                                                                    |                                                                                                                                                cAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCggg                                                                                                                                               >  8:342598/1‑149 (MQ=255)  aaGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCTGAAACT‑TGCCGAAACC‑‑TGTGGGAGCGGGCAt                                                                                                                                            >  8:160008/1‑149 (MQ=255)    gACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCAt                                                                                                                                            >  1:384711/1‑149 (MQ=255)       cATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGcc                                                                                                                                         <  6:203492/149‑1 (MQ=255)       cATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGcc                                                                                                                                         <  2:436801/149‑1 (MQ=255)       cATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCAATGTGGGAGCGGCCATGcc                                                                                                                                         >  5:362229/1‑149 (MQ=255)              aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AAc                                                                                                                                 <  4:316127/149‑1 (MQ=255)                 cacaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACggg                                                                                                                              >  7:296255/1‑149 (MQ=255)                  acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGggc                                                                                                                             >  8:248712/1‑149 (MQ=255)                  acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGggc                                                                                                                             >  6:222712/1‑149 (MQ=255)                      ggCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCggg                                                                                                                                               <  5:181141/128‑1 (MQ=255)                      ggCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCggg                                                                                                                                               >  6:181141/1‑128 (MQ=255)                      ggCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGggcctgg                                                                                                                         <  6:386932/149‑1 (MQ=255)                       ccACGCCGGAGGCACACGTTCACACTCAACGCGCTGGCGGAGCGGGAGAAGTACGCCATGGACCCCAAGCTGATCTGATTGCGACATACGGGGGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGggcctggc                                                                                                                        <  4:292119/148‑1 (MQ=255)                          cGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGgcctggcctg                                                                                                                     <  6:290372/149‑1 (MQ=255)                           gCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑CACGGGCCTGGCctgc                                                                                                                    >  3:65908/1‑149 (MQ=255)                                 tGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGAtct                                                                                                              <  8:296255/149‑1 (MQ=255)                                  tcAGAAGTTGAAAGTTAACTCGCTGGCGGAGCTGGTGAAGTAGGGCATGGATCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGTAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCctgct                                                                                                                   <  8:139308/142‑1 (MQ=255)                                  gCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCctgct                                                                                                                   >  7:139308/1‑143 (MQ=255)                                  gCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGAtctc                                                                                                             >  1:120551/1‑149 (MQ=255)                                    aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACgg                                                                                                                               <  5:82132/129‑1 (MQ=255)                                    aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACgg                                                                                                                               >  6:82132/1‑129 (MQ=255)                                             aaGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGc                                                                                                  >  6:437174/1‑149 (MQ=255)                                                 gAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGAGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGc                                                                                              >  5:436632/1‑149 (MQ=255)                                                  aaCTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGc                                                                                              <  5:222712/148‑1 (MQ=255)                                                       gCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTc                                                                                        <  5:437174/149‑1 (MQ=255)                                                          ggCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTcgcg                                                                                     <  7:248712/149‑1 (MQ=255)                                                            cGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGGGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCggg                                                                                   <  8:117705/149‑1 (MQ=255)                                                             ggAGCTTGTGAATTACGCCATGGAGCACAAGCTTATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTAt                                                                                                          <  6:182230/125‑1 (MQ=255)                                                             ggAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATg                                                                                                         <  1:124388/126‑1 (MQ=255)                                                             ggAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATg                                                                                                         >  2:124388/1‑126 (MQ=255)                                                             ggAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATATCTAt                                                                                                          >  5:182230/1‑125 (MQ=255)                                                                 cTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCAAGCCCCCGCAACGGG‑CGGGGCGGGTGATGTATATTGGTGAGACGGCCGCATAGCGGGccatc                                                                              >  5:32651/1‑145 (MQ=255)                                                                      gAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCAGGCCGGCTGATCTCTATGGCAGAGCCGGCCTCATCGCGGGCAT‑GCCCGCt                                                                        >  2:119877/1‑149 (MQ=255)                                                                       aaGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCAAGCCCCCG‑CACGGGCCAGGCCTGCTGAACACTATGGCTGACCCGGCCTCTTCGAGTGCAT‑GCCCCCTc                                                                       >  6:227839/1‑149 (MQ=255)                                                                            cGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATTCCCGCG‑GACGGGCCTGGCCTGCTGATGTCTATGGCTGAGCCGGCCACTTCGCGGGCCT‑TCCCGCTCCca                                                                    >  3:98221/1‑147 (MQ=255)                                                                             gCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAg                                                                                                   >  6:210790/1‑116 (MQ=255)                                                                             gCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAg                                                                                                   <  5:210790/116‑1 (MQ=255)                                                                                   caGCACACGCTTATCTGATTGCGACATCGGGGTGCCCTAAACT‑TGCCGACGCCTATGTGGGAGCGGGCAGGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCg                                                           <  4:65908/148‑1 (MQ=38)                                                                                    aGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCCCG‑AACGGGCCTGGGCTGCTGGTCTCTATTGCGGCGCCGGCCGCTTAGCGGGCAT‑TCCCGCGCCCACAGGGTTAGt                                                          >  7:340509/1‑149 (MQ=255)                                                                                               atctgatTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGGTTCGTGGTTGGGTCgg                                               >  1:279114/1‑148 (MQ=255)                                                                                                  tgatTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAg                                            >  1:75397/1‑149 (MQ=255)                                                                                                     ttGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGAtct                                                                                                              >  5:157870/1‑81 (MQ=255)                                                                                                     ttGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGAtct                                                                                                              <  6:157870/81‑1 (MQ=255)                                                                                                       gCGACATACGGG‑GCCCCCAACTGTGCCGATCCCTTTGGGGCCGGGGGCATGCCCGCG‑AACGGGCCGGGCCTGATTATCTCTCTGGCGGAGCCGGCCCCTTCGCGGGAAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCa                                        <  6:362229/148‑1 (MQ=255)                                                                                                         gACATCCGGGTGCCCGAAAAT‑TCGCGCCTCCTATGTGGTCGCGGGCAGGCGCGCG‑AACGGGCCCGCCCTGCTGATCTCTAGGGCTCACCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTc                                     <  5:227839/149‑1 (MQ=25)                                                                                                           cttccGGGGGCCCCATCCT‑TGCCGCGGCATTTGTGGGCGCGGGCTTCCCGGCT‑ATGGGGCCTGGCGTGCTGATCTTTTGGGCTGAGCGGCCGTATTCGC‑GGCATGGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTcc                                    <  2:384711/144‑1 (MQ=255)                                                                                                             tACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGAAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAAt                                 <  2:75397/149‑1 (MQ=255)                                                                                                                  gTGCCCGAAACA‑TGCCGACGCCTATGGGGGAGCGGGCATGCCCGCT‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGc                            <  7:342598/149‑1 (MQ=39)                                                                                                                     cccTAAACT‑TGCCGAAGCCTATGTGGTCGCGGGCATGCCCGCG‑AACGGGCCTGGCCTTCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCAt                         <  6:458157/149‑1 (MQ=39)                                                                                                                            cT‑TGCCGAAGCCTTTGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTa                  <  1:119877/149‑1 (MQ=255)                                                                                                                                    aaGCCTATGTGGGAGCGGGCATGCCCGCG‑AACGGGCCTGGGCGGCTGATCTGTATGGCGGCGGCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGGTCGCAAGGGCATTCGCCACCCGGCCTCCTTGTTGGGCggt           >  7:216459/1‑147 (MQ=255)                                                                                                                                         tATGTGGGAGCGGGCATGCCCGCG‑CACGGGCCTGGCCTGCTGATCTCTATGGCTGCGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGGTTGGTGGTTGGCTCGCCAGGGCATTGCAATCCCGCCATCCATGTAGGGCGATCCCTa      >  5:309505/1‑149 (MQ=38)                                                                                                                                              gggAGCGGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCCTGTAGGGCGATCCCTacaac  >  6:451113/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACT‑TGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCG‑AACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAT‑GCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAAC  >  NC_002947/499057‑499344

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: ‑