Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,426,561	G→A	8.1%	H111H (CAC→CAT)	PP_2127 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,426,561	0	G	A	8.1%	140.0 / 2.2	49	H111H (CAC→CAT)	PP_2127	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (24/21);  new base A (2/2);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.95e-01

GGAAACATCGCGCACGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAG  >  NC_002947/2426420‑2426707                                                                                                                                              |                                                                                                                                                      ggAAACATCGCGCACGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGtt                                                                                                                                                >  3:250590/1‑149 (MQ=255) ggAAACATCGCGCACGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGtt                                                                                                                                                >  4:204116/1‑149 (MQ=255)           cgcACGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGcc                                                                                                                                         >  2:171018/1‑146 (MQ=255)              aCGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATg                                                                                                                                   >  7:234685/1‑149 (MQ=255)                       aGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTc                                                                                                                          <  3:81680/149‑1 (MQ=255)                          gtgtCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGtc                                                                                                                       >  4:256151/1‑149 (MQ=255)                               aTCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTcttctt                                                                                                                  >  5:304775/1‑149 (MQ=255)                                tCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCt                                                                                                                                 <  8:129948/133‑1 (MQ=255)                                tCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCt                                                                                                                                 >  7:129948/1‑133 (MQ=255)                                 ccAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTg                                                                                                                 >  6:248182/1‑148 (MQ=255)                                  cAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCa                                                                                                               >  7:67593/1‑149 (MQ=255)                                   aGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCa                                                                                                               >  1:192204/1‑148 (MQ=255)                                   aGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCa                                                                                                               <  2:192204/148‑1 (MQ=255)                                      gTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCtt                                                                                                           <  4:250590/149‑1 (MQ=255)                                       tgctgcGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTg                                                                                                          <  1:97155/149‑1 (MQ=255)                                            cgcAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGGAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGc                                                                                                       <  1:171018/147‑1 (MQ=255)                                                    gTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCgg                                                                                             <  3:243089/149‑1 (MQ=255)                                                                cTGCAACTCGTCGGGCATGCGCCGTTTCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCATGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑g                                                                               >  1:170095/1‑149 (MQ=255)                                                                cTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCATGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑g                                                                               >  1:164968/1‑149 (MQ=255)                                                                   cAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGgc                                                                            <  4:233348/149‑1 (MQ=255)                                                                     aCTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGgcg                                                                           >  2:14194/1‑148 (MQ=255)                                                                         gtcgGGCATGCGGCGTTGCCGCCCCGGGAGTTGCAGCTTGGCAGGGGTGAGCGGTTGACCGATGTCGTCGTGCAGTTGCCGGCCCAGATGCTGGCGCGGGTGTTCTTGCACCTTGAGCATGCGCGCGGCC‑CGCGCGGCC‑GGGGG‑CAGGt                                                                     >  2:295884/1‑149 (MQ=255)                                                                         gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCTGGgcg‑ccag                                                                      >  7:112864/1‑146 (MQ=255)                                                                         gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAgg                                                                      <  1:14194/148‑1 (MQ=255)                                                                         gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAg                                                                       <  2:116198/147‑1 (MQ=255)                                                                         gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGt                                                                     <  5:248182/149‑1 (MQ=255)                                                                          tcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGTTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTg                                                                    >  5:80452/1‑149 (MQ=255)                                                                            gggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCC‑GAGCG‑Catgctc                                                                   <  6:304775/148‑6 (MQ=255)                                                                             ggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTgg                                                                   <  6:75537/147‑1 (MQ=255)                                                                             ggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTgg                                                                   >  5:75537/1‑147 (MQ=255)                                                                                 tGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGAc                                                             >  4:308889/1‑149 (MQ=255)                                                                                           cAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgccca                                                   <  3:204116/149‑1 (MQ=255)                                                                                           cAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCATGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgccca                                                   <  2:164968/149‑1 (MQ=255)                                                                                           cAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCATGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgccca                                                   <  2:170095/149‑1 (MQ=255)                                                                                             gCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgcccagg                                                 <  1:295884/149‑1 (MQ=255)                                                                                             gCCACTGCAGTTGCAGCTTGGCAGCAGTGAGCAGCTGACCGATGGCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgcccagg                                                 <  7:201876/149‑1 (MQ=255)                                                                                              ccACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCTGGGCGCCAGGTCGATCCACCT‑GCgcccggc                                                 <  8:112864/149‑4 (MQ=38)                                                                                                  tGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgcccaggcccag                                            >  2:230198/1‑149 (MQ=255)                                                                                                    cAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGtt                                          >  4:204098/1‑149 (MQ=255)                                                                                                      gTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTg                                         >  7:112020/1‑148 (MQ=255)                                                                                                        tGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTa                                       <  3:308889/148‑1 (MQ=255)                                                                                                         gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgcccaggcccag                                            >  2:192956/1‑142 (MQ=255)                                                                                                         gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCgcccaggcccag                                            <  1:192956/142‑1 (MQ=255)                                                                                                           aGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaac                                   <  1:230198/149‑1 (MQ=255)                                                                                                           aGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGAGCGACCTGGCGCCCAGGCCCAGTTGTacaac                                   <  8:234685/149‑1 (MQ=255)                                                                                                            gCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaa                                    >  3:251650/1‑147 (MQ=255)                                                                                                                ggCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCAc                              >  3:25325/1‑149 (MQ=255)                                                                                                                            cAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGa                  >  2:51836/1‑149 (MQ=255)                                                                                                                                    cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACCGCACCCAGCGTGGCGACCAACTg           >  8:168224/1‑148 (MQ=255)                                                                                                                                         tcgtcgTGCAGTTCCCGGCCCCGATCCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCAc     <  8:67593/149‑1 (MQ=255)                                                                                                                                            tcgtGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACcag  >  3:231275/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                                      GGAAACATCGCGCACGTTACCGAGGGTGTCATCCAGCGTGCTGCGCAGGGCGTCGCAGTGCCCCTGCAACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCC‑GGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAG  >  NC_002947/2426420‑2426707

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑