Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,349,185	A→G	7.7%	N498S (AAC→AGC) ‡	PP_2944 →	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,349,185	0	A	G	7.7%	144.1 / 2.6	52	N498S (AAC→AGC) ‡	PP_2944	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (24/24);  new base G (2/2);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.40e-01

GCCGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGC  >  NC_002947/3349039‑3349328                                                                                                                                                   |                                                                                                                                                gCCGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAAc                                                                                                                                                <  3:374008/148‑1 (MQ=255)  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)                                                                                                                                                   |                                                                                                                                                GCCGCTGTCGGTCAACGACCTGGTCGAGGACGCGCTGCGCATGAACGCAGGCGCGTTGACCCGGCATCAAGTGAGGGTAGTGCGCGACTTCGCAGATCTGCCTCTGGTGATGGGCGACCGGCATCGGCTGTTGCTGATTCTGATCAACCTGATCAGCAACGCCAAGTACGCCATGTCCGGCCCCGGCAGCGACCCGCGGACGATGATCCTCAGGACGCGCATCGTTGAGGGGGGCTTGCTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGC  >  NC_002947/3349039‑3349328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑