Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,477,321	T→A	9.4%	Q224L (CAG→CTG)	PP_3968 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,477,321	0	T	A	9.4%	142.1 / 5.3	53	Q224L (CAG→CTG)	PP_3968	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (23/25);  new base A (2/3);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.78e-01

AATCAAATTGGAGAAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTGTCGCAGGA  >  NC_002947/4477173‑4477465                                                                                                                                                     |                                                                                                                                                  aaTCAAATTGGAGAAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACctgct                                                                                                                                                   >  8:270111/1‑149 (MQ=255)   tCAAATTGGAGAAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACctgctg                                                                                                                                                  >  4:26079/1‑148 (MQ=255)     aaaTTGGAGAAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAg                                                                                                                                               <  3:330867/149‑1 (MQ=255)           gagaAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCAGCAGGTggag                                                                                                                                         <  2:214296/149‑4 (MQ=255)            agaagaCCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCAGCAGGTggagc                                                                                                                                        <  8:23930/149‑5 (MQ=255)             gaagaCCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑g                                                                                                                                      >  2:199110/1‑149 (MQ=255)              aagaCCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑gg                                                                                                                                     >  1:70192/1‑149 (MQ=255)                    tGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATAcc                                                                                                                               >  7:250571/1‑149 (MQ=255)                      aGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCt                                                                                                                              <  2:4826/148‑1 (MQ=255)                         cATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTc                                                                                                                          <  7:270111/149‑1 (MQ=255)                               aTCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAAt                                                                                                                    >  5:80311/1‑149 (MQ=255)                                   ggATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACa                                                                                                                <  7:336027/149‑1 (MQ=255)                                    gATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAg                                                                                                               >  3:79948/1‑149 (MQ=255)                                      taaaaCTAACCGATGATCTATACGGATTCGTTCAAAATAATGTTAGACCAAGGGGAACCCGCGAGCAGTTCATAGATGCCCTATCGACAGATCGGGTTCAGATCCAAATGCTGCAGGTGCAAC‑GGGATACCGGTACCAAAAATACatcc                                                                                                             >  8:55490/3‑146 (MQ=255)                                      tCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAgcg                                                                                                             >  6:339959/1‑149 (MQ=255)                                                cGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATcc                                                                                                   <  5:339959/149‑1 (MQ=255)                                                       cTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCACGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGt                                                                                            >  5:132358/1‑149 (MQ=255)                                                          taaggATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGAGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGTTGCACC‑GGGATACCTGTTCCCAAACTACAGCGCGCCAGATCCAGAAg                                                                                              <  7:55490/141‑1 (MQ=255)                                                            cGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGtt                                                                                        >  2:287175/1‑148 (MQ=255)                                                                   gTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCAGCAGGTg                                                                                                                                            <  1:185751/90‑1 (MQ=255)                                                                   gTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCAGCAGGTg                                                                                                                                            >  2:185751/1‑90 (MQ=255)                                                                    ttCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATAtt                                                                               >  8:142158/1‑149 (MQ=255)                                                                    ttCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATAtt                                                                               >  3:91731/1‑149 (MQ=255)                                                                       aaaaTAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCTGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATAttgtt                                                                            >  2:111709/1‑149 (MQ=255)                                                                       aaaaTAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATAttgtt                                                                            <  4:79948/149‑1 (MQ=255)                                                                        aaaTAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATAttgttg                                                                           >  3:309530/1‑149 (MQ=255)                                                                              tGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCgg                                                                     >  2:301400/1‑149 (MQ=255)                                                                              tGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCgg                                                                     <  8:198855/149‑1 (MQ=255)                                                                                      cAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCt                                                             >  8:91303/1‑149 (MQ=255)                                                                                       aaGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTg                                                            <  4:91731/149‑1 (MQ=255)                                                                                        aGGGGAACCCGCGCGCAGTTCCTCGATCCCCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGAGCACC‑GGCATACCTGTTCCCAAAATACAGCGAGCCAGATCCAGAAGCACGTTCACCATATTGTAGGCACCGCGAGCGATga                                                           >  3:244693/1‑148 (MQ=255)                                                                                         ggggAACCCGCGCGCAGTTCCTCGATGAGCGAGCTTCAGATCGGGTTCAGCTCCAGCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATGCTGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTg                                                            <  3:142892/147‑1 (MQ=255)                                                                                         cgggAACCCGCGCGCAGGTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGtt                                                          <  8:137034/148‑1 (MQ=255)                                                                                           ggAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTa                                                         >  4:357463/1‑148 (MQ=255)                                                                                             aaCCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACaa                                                      <  1:199110/149‑1 (MQ=255)                                                                                                   cgcgcAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCt                                                  >  5:40222/1‑147 (MQ=255)                                                                                                        aGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAgcggc                                           <  1:301400/149‑1 (MQ=255)                                                                                                          ttCCTCGATGACGGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGa                                         <  8:250571/149‑1 (MQ=255)                                                                                                                gATGACCGAGCGACAGATGGGGTTCAGCTCCGCGTGCTGCAGGTGCAGC‑GGGATAGCTGTTCCCAATTTACAGCGCGCGTGTTCGAGATGGTCGTTCAGGATATTGTTGGCCCGGCGAGGGCGGTTACGGACCTGAgcggcgcggaggg                                   >  6:315876/1‑142 (MQ=255)                                                                                                                 aTGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGttt                                  <  6:132358/149‑1 (MQ=255)                                                                                                                 aTGACCGAGCGACAGATCGGGTTCAGCTCCACATGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGAGCGCCAGATCCAGAAGGTCGTTAACCATATAGTTTGCCCGGCGAGAGCTGTTACAAACATGAGCGGCGAGCAGtat                                  >  2:161390/1‑147 (MQ=255)                                                                                                                    aCCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTAc                               <  3:26079/149‑1 (MQ=255)                                                                                                                    aCCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGACGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTAc                               <  2:70192/149‑1 (MQ=255)                                                                                                                       gAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCtt                            <  6:80311/149‑1 (MQ=255)                                                                                                                             cAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCAcc                      >  3:349677/1‑149 (MQ=255)                                                                                                                              aGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCt                     <  1:287175/149‑1 (MQ=255)                                                                                                                               gATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCt                     >  3:268575/1‑148 (MQ=255)                                                                                                                                 tCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGAc                  <  7:142158/149‑1 (MQ=255)                                                                                                                                   gggTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGGCt                 <  4:309530/148‑1 (MQ=255)                                                                                                                                    ggTTCAGCTCCACCTGCTGCAGGTGCACC‑GTGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATTTTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGTCGAGCAGTTTTACCTTCTCACCTGACTCa               <  1:161390/149‑1 (MQ=255)                                                                                                                                         cggtgcACCTGCAGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTg          >  5:81834/6‑149 (MQ=255)                                                                                                                                          gCTCCACCTGCTGCAGGTGCACCGGGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCAt              >  1:3152/1‑145 (MQ=255)                                                                                                                                          gCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCAt              <  2:3152/144‑1 (MQ=255)                                                                                                                                              cACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTGTCg       <  7:91303/147‑1 (MQ=255)                                                                                                                                              cACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTGTCGCa     <  3:357463/149‑1 (MQ=255)                                                                                                                                                 ctgctgCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTGTCGCAGGa  <  5:315876/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  AATCAAATTGGAGAAGACCTGAGCCATGCGATCAGGATCAAACTGACCGGTGATCTGTACGGATTCGTTCAAAATAATGTTCGCCCAAGGGGAACCCGCGCGCAGTTCCTCGATGACCGAGCGACAGATCGGGTTCAGCTCCACCTGCTGCAGGTGCACC‑GGGATACCTGTTCCCAAATTACAGCGCGCCAGATCCAGAAGGTCGTTCACCATATTGTTGGCCCGGCGAGCGCTGTTACAAACCTGAGCGGCGAGCAGTTTTACCTTCTCACCTGACTCATCCTGTCGCAGGA  >  NC_002947/4477173‑4477465

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: ‑