Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,289,430	T→G	8.0%	K1053Q (AAG→CAG)	PP_3761 ←	two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,289,430	0	T	G	8.0%	145.8 / 2.6	48	K1053Q (AAG→CAG)	PP_3761	two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (24/20);  new base G (2/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCTGGCGGATCAGGCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCTGCGATTC  >  NC_002947/4289287‑4289568                                                                                                                                                 |                                                                                                                                           ttGCTGGCGGATCAGGCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTAGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCt                                                                                                                                       >  6:213788/1‑149 (MQ=255)       gCGGATCAGGCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCCGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAggg                                                                                                                                 >  2:329265/1‑149 (MQ=255)       gCGGATCAGGCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAggg                                                                                                                                 <  7:301172/149‑1 (MQ=255)                gCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGt                                                                                                                          >  1:127320/1‑147 (MQ=255)                  gggTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAgg                                                                                                                      <  4:291834/149‑1 (MQ=255)                    gTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATGTGCGCCCTTGTGCTCCAGGGCGCTGGTCAggg                                                                                                                     <  1:219380/149‑1 (MQ=255)                         cTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTtgt                                                                                                                                          >  6:134896/1‑122 (MQ=255)                         cTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTtgt                                                                                                                                          <  5:134896/122‑1 (MQ=255)                            gAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGatat                                                                                                            >  8:132136/1‑149 (MQ=255)                            gAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTACAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTACAGGTCTCTGGGCAGGTCAAatatat                                                                                                            >  4:315069/1‑149 (MQ=255)                             aaGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATAtt                                                                                                           <  6:280295/149‑1 (MQ=255)                                        ctcCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTGGAGCACAAGGgcg                                                                                                                               >  6:145640/1‑118 (MQ=255)                                        ctcCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTGGAGCACAAGGgcg                                                                                                                               <  5:145640/118‑1 (MQ=255)                                             gCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTcc                                                                                           <  5:12374/149‑1 (MQ=255)                                                  atcaCGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTccacca                                                                                       <  7:132136/148‑1 (MQ=255)                                                  atcaCGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACcag                                                                                      >  3:21216/1‑149 (MQ=255)                                                    caCGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACcag                                                                                      >  5:368159/1‑147 (MQ=255)                                                            tCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTg                                                                            <  2:127320/149‑1 (MQ=255)                                                                  ccAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGccc                                                                      >  6:364909/1‑149 (MQ=255)                                                                   cAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCt                                                                     >  1:16776/1‑149 (MQ=255)                                                                     ggTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGcc                                                                       >  4:332667/1‑145 (MQ=255)                                                                     ggTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGcc                                                                       <  3:332667/145‑1 (MQ=255)                                                                     ggTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTc                                                                    >  4:53634/1‑148 (MQ=255)                                                                      gTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCg                                                                   >  7:136950/1‑148 (MQ=255)                                                                       tCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGCCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGaa                                                                 <  2:107773/149‑1 (MQ=255)                                                                                        ctCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTgc                                                >  1:25587/1‑149 (MQ=255)                                                                                          ccAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGAGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTgcgc                                              >  8:96864/1‑149 (MQ=255)                                                                                           cAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTgcgcg                                             >  8:104276/1‑149 (MQ=255)                                                                                           cAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTgcgcg                                             >  6:363175/1‑149 (MQ=255)                                                                                           cAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTgcgcg                                             >  3:140734/1‑149 (MQ=255)                                                                                              gcgcTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCtt                                                                             <  3:129579/114‑1 (MQ=255)                                                                                              gcgcTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCtt                                                                             >  4:129579/1‑114 (MQ=255)                                                                                              gcgcTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCgg                                          <  3:53634/149‑1 (MQ=255)                                                                                                   cGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTg                                     >  4:308147/1‑149 (MQ=255)                                                                                                    gATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCtt                                      <  7:104276/147‑1 (MQ=255)                                                                                                    gATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCtt                                      <  4:21216/147‑1 (MQ=255)                                                                                                    gATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCtt                                      <  4:140734/147‑1 (MQ=255)                                                                                                    gATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGa                                    <  5:364909/149‑1 (MQ=255)                                                                                                     aTGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAg                                   <  8:136950/149‑1 (MQ=255)                                                                                                          ttCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGc                              >  5:100099/1‑149 (MQ=255)                                                                                                                cccGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGAc                        <  1:19762/149‑1 (MQ=255)                                                                                                                cccGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGGCTTGAGCATGCGTTGAc                        >  4:75771/1‑149 (MQ=255)                                                                                                                                tCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCt         <  5:228787/148‑1 (MQ=255)                                                                                                                                    cAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCTGCGAt    >  1:140052/1‑149 (MQ=255)                                                                                                                                     aaTG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCTGCGAtt   >  2:222075/1‑149 (MQ=255)                                                                                                                                      aTG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCTGCGATTc  <  5:213788/149‑1 (MQ=255)                                                                                                                                          gcgcCCTGGAGCACAAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAg                                   <  2:321240/113‑1 (MQ=255)                                                                                                                                          gcgcCCTGGAGCACAAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAg                                   >  1:321240/1‑113 (MQ=255)                                                                                                                                            gcCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGCTGAc                        >  4:45946/1‑122 (MQ=255)                                                                                                                                            gcCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGCTGAc                        <  3:45946/122‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                           TTGCTGGCGGATCAGGCGGGTGGCCTCGAAGCCGTCCATCTCCGGCATCATCACGTCCATCAGCACCAGGTCGATATCGTCGTGCTGCTCCAGGCGCTCGATGGCTTCGCGCCCGTTGCGGCCGATTTCGACAATG‑GCGCCCTTGTGCTCCAGGGCGCTGGTCAGGGCAAAGATATTACGCACATCGTCGTCCACCAGCAGCACCTTGCGGCCCTCGAACACCTTGTCGCGGCTGCGCGCGGTCTTGAGCATGCGTTGACGTTCGTTGGACAGCTGCGATTC  >  NC_002947/4289287‑4289568

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: ‑