Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,349,187	C→T	7.8%	L499L (CTG→TTG)	PP_2944 →	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,349,187	0	C	T	7.8%	147.3 / 2.2	51	L499L (CTG→TTG)	PP_2944	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base T (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.72e-01

CCGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAG  >  NC_002947/3349040‑3349330                                                                                                                                                    |                                                                                                                                                ccGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCt                                                                                                                                                >  2:185476/1‑149 (MQ=255)   gCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGa                                                                                                                                              >  8:102350/1‑149 (MQ=255)    cTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGAt                                                                                                                                             <  5:162174/149‑1 (MQ=255)       tCGGTCAACGACCTTGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCa                                                                                                                                           <  3:264398/148‑1 (MQ=255)                gACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCaa                                                                                                                                 <  7:102350/149‑1 (MQ=255)                gACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCaa                                                                                                                                 <  6:117037/149‑1 (MQ=255)                gACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCaa                                                                                                                                 <  7:382111/149‑1 (MQ=255)                      gTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACg                                                                                                                            <  6:26325/148‑1 (MQ=255)                      gTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACg                                                                                                                            >  5:26325/1‑148 (MQ=255)                      gTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGc                                                                                                                           >  2:286855/1‑149 (MQ=255)                         gAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAGGTTGATCAgaatt                                                                                                                                      <  2:318657/135‑5 (MQ=255)                         gAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAGGTTGATCAgaatt                                                                                                                                      <  2:323639/135‑5 (MQ=255)                         gAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAGGTTGATCAgaatt                                                                                                                                      >  1:323639/1‑131 (MQ=255)                         gAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAGGTTGATCAgaatt                                                                                                                                      >  1:318657/1‑131 (MQ=255)                         gAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCGGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCAt                                                                                                                        >  8:270361/1‑149 (MQ=255)                                      gcATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGc                                                                                                           <  7:51221/149‑1 (MQ=255)                                        aTGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAg                                                                                                         >  7:98023/1‑149 (MQ=255)                                            aCGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGAc                                                                                                     <  1:185476/149‑1 (MQ=255)                                                      gTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACga                                                                                           >  4:397172/1‑149 (MQ=255)                                                      gTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACg                                                                                            >  8:342795/1‑148 (MQ=255)                                                          aCCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACgatgat                                                                                       >  8:316610/1‑149 (MQ=255)                                                           cccGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATc                                                                                      <  7:121161/149‑1 (MQ=255)                                                                  tCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGa                                                                               >  6:400559/1‑149 (MQ=255)                                                                  tCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGa                                                                               <  7:316610/149‑1 (MQ=255)                                                                      gTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATc                                                                                                                                            <  8:327861/84‑1 (MQ=255)                                                                      gTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATc                                                                                                                                            >  7:327861/1‑84 (MQ=255)                                                                       tGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGAcgcg                                                                           >  7:216506/1‑148 (MQ=255)                                                                          gggTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATc                                                                       <  2:16900/149‑1 (MQ=255)                                                                            gTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCAGGCCCCGGCAGCGACCCGCGGAGCATGCTCCTCAGGACGCTCATCga                                                                     >  5:299406/1‑148 (MQ=255)                                                                             tAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGtt                                                                    <  6:404519/149‑1 (MQ=255)                                                                              aGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGtt                                                                    >  8:203765/1‑148 (MQ=255)                                                                               gTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCa                                                                                  >  4:137178/1‑133 (MQ=255)                                                                               gTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCa                                                                                  <  3:137178/133‑1 (MQ=255)                                                                                tGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAg                                                                 <  7:342795/149‑1 (MQ=255)                                                                                tGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAg                                                                 <  8:98023/149‑1 (MQ=255)                                                                                       cTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCGGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCt                                                          <  7:270361/149‑1 (MQ=255)                                                                                        ttCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCtt                                                         >  4:318237/1‑149 (MQ=255)                                                                                            cAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTg                                                     >  8:307707/1‑149 (MQ=255)                                                                                                    ccTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAg                                             >  6:187252/1‑149 (MQ=255)                                                                                                     ctctGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGc                                            <  5:400559/149‑1 (MQ=255)                                                                                                          gcgctGGGCGACCGGCATCGGCGGTTGCTGATGCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCt                                       <  6:285898/145‑1 (MQ=255)                                                                                                                   gACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAggg                              <  3:397172/149‑1 (MQ=255)                                                                                                                      cGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCg                            >  8:214236/1‑148 (MQ=255)                                                                                                                        gCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAg                         >  1:12293/1‑149 (MQ=255)                                                                                                                                  ttGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGcccc               >  5:103865/1‑149 (MQ=255)                                                                                                                                    gCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCt              <  8:216506/148‑1 (MQ=255)                                                                                                                                     cTGATTCTGATCAACCTGATAAGCAACGCAAAGTACGCCATGTCCCGCCCCGGCAGCGACCCGCGCACGAAGATCCTCAGGACGCGCATCGTTGAGGGGTGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAATGCATTGCCCCtc             >  8:269549/1‑147 (MQ=255)                                                                                                                                            tGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCg                            <  2:17863/126‑1 (MQ=255)                                                                                                                                            tGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCg                            >  1:17863/1‑126 (MQ=255)                                                                                                                                             gATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTg     >  6:62024/1‑148 (MQ=255)                                                                                                                                              aTCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGc    <  3:318237/148‑1 (MQ=255)                                                                                                                                                   ccTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTg             >  5:240778/1‑134 (MQ=255)                                                                                                                                                   ccTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTg             <  6:240778/134‑1 (MQ=255)                                                                                                                                                   ccTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCag  >  7:92529/1‑145 (MQ=255)                                                                                                                                                    |                                                                                                                                                CCGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAG  >  NC_002947/3349040‑3349330

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: ‑