Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,872,138	A→T	7.5%	H81Q (CAT→CAA)	PP_3420 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,872,138	0	A	T	7.5%	155.3 / 3.3	53	H81Q (CAT→CAA)	PP_3420	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (27/22);  new base T (2/2);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

CGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCACCGA  >  NC_002947/3872006‑3872284                                                                                                                                      |                                                                                                                                                   cGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCt                                                                                                                                    >  3:3824/1‑149 (MQ=255)  ggCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGTCCGGTGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTg                                                                                                                                   <  4:223264/149‑1 (MQ=255)   gCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                                  <  8:53023/149‑1 (MQ=255)     aGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGc                                                                                                                                <  2:28122/149‑1 (MQ=255)       gTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCa                                                                                                                              >  2:136271/1‑149 (MQ=255)           tCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGc                                                                                                                          >  5:223022/1‑149 (MQ=255)             gACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                                  <  3:243827/139‑1 (MQ=255)             gACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                                  >  4:243827/1‑139 (MQ=255)                    tCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGcc                                                                                                                               >  5:89208/1‑135 (MQ=255)                    tCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGcc                                                                                                                               <  6:89208/135‑1 (MQ=255)                       aGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTg                                                                                                              >  7:191982/1‑149 (MQ=255)                           aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                              <  4:46728/113‑1 (MQ=255)                           aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                              >  3:46728/1‑113 (MQ=255)                               gATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGt                                                                                                        >  8:235222/1‑147 (MQ=255)                               gATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTaa                                                                                                      <  1:136271/149‑1 (MQ=255)                                aTCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGCACTGCGCGGTAAg                                                                                                     <  4:3824/149‑1 (MQ=255)                                    gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                                 <  7:235222/149‑1 (MQ=255)                                    gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                                 >  2:40364/1‑149 (MQ=255)                                    gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                                 <  1:43887/149‑1 (MQ=255)                                                  aGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCAc                                                                                   >  3:55915/1‑149 (MQ=255)                                                              aCCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGca                                                                        <  5:21554/148‑1 (MQ=255)                                                                cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                     <  6:223022/149‑1 (MQ=255)                                                                cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                     >  2:243033/1‑149 (MQ=255)                                                                cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                     >  5:101440/1‑149 (MQ=255)                                                                  gCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTcgc                                                                           <  6:104731/141‑1 (MQ=255)                                                                  gCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTcgc                                                                           >  5:104731/1‑141 (MQ=255)                                                                   cAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcaccac                                                                    <  4:55915/147‑1 (MQ=255)                                                                            cAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTc                                                          <  1:243033/148‑1 (MQ=255)                                                                              ggTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGa                                                        >  3:80553/1‑148 (MQ=255)                                                                               gTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGGTTGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGa                                                        >  1:44361/1‑148 (MQ=255)                                                                                    gCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTaa                                                 >  1:129129/1‑149 (MQ=255)                                                                                     ccGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAAc                                                <  2:129129/149‑1 (MQ=255)                                                                                     ccGCGGGTCCAGAAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTTAGAATGCAGCACTTAGGCCTGGGCCATTGCATGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCAAGAAGCGCGTCGAAACGTAAc                                                >  2:241287/1‑149 (MQ=255)                                                                                       gcgGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGACCTGCGCGGTAAGCATGGCATCGCGCTCCCCGCTGTCGCGCACCACGACGCGCGTCGAAACCTCAcc                                               >  5:195819/1‑148 (MQ=255)                                                                                                     tCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCAc                                >  8:75291/1‑149 (MQ=255)                                                                                                       gCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                                 <  5:34854/82‑1 (MQ=255)                                                                                                       gCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                                 >  6:34854/1‑82 (MQ=255)                                                                                                         ccATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAg                            >  2:218541/1‑149 (MQ=255)                                                                                                          cATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAgg                           >  3:20216/1‑149 (MQ=255)                                                                                                          cATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAgg                           >  6:99768/1‑149 (MQ=255)                                                                                                             ggtgg‑tGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTaa                        >  7:47064/1‑149 (MQ=255)                                                                                                               tgg‑tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAAt                       >  8:221884/1‑148 (MQ=255)                                                                                                               tgg‑tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATg                      <  4:20216/149‑1 (MQ=255)                                                                                                                   tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATc                   <  2:44361/149‑1 (MQ=255)                                                                                                                   tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATc                   <  7:75291/149‑1 (MQ=255)                                                                                                                     ccAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCaa                 >  2:177664/1‑149 (MQ=255)                                                                                                                     aagtgcggcATTCGCAATTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGt                                                           >  6:199786/5‑107 (MQ=255)                                                                                                                     aagtgcggcATTCGCAATTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGt                                                           <  5:199786/103‑1 (MQ=255)                                                                                                                          cggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTg                                                                               <  6:252320/82‑1 (MQ=255)                                                                                                                          cggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTg                                                                               >  5:252320/1‑82 (MQ=255)                                                                                                                           ggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCt           <  5:99768/149‑1 (MQ=255)                                                                                                                                ttGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCa      >  6:227350/1‑149 (MQ=255)                                                                                                                                  gCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCAc     <  1:105447/148‑1 (MQ=255)                                                                                                                                     aaTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCACCGa  >  4:238297/1‑148 (MQ=255)                                                                                                                                     aaTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCACCGa  >  8:67286/1‑148 (MQ=255)                                                                                                                                      |                                                                                                                                                   CGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCACCGA  >  NC_002947/3872006‑3872284

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: ‑