Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,763,086	A→T	14.8%	H110L (CAT→CTT)	PP_3326 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,763,086	0	A	T	14.8%	127.6 / 14.5	54	H110L (CAT→CTT)	PP_3326	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (30/16);  new base T (4/4);  total (34/20)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01

GGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGACGCTG  >  NC_002947/3762939‑3763234                                                                                                                                                    |                                                                                                                                                      ggAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCAt                                                                                                                                                      >  1:115891/1‑149 (MQ=255)    aCATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGt                                                                                                                                                    >  3:280699/1‑148 (MQ=255)      aTGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACat                                                                                                                                                 >  2:103047/1‑148 (MQ=255)      aTGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCaa                                                                                                                                                 <  2:264287/149‑1 (MQ=255)         aTCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATgg                                                                                                                                               <  2:382069/148‑1 (MQ=255)              ggTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGa                                                                                                                                         >  8:152403/1‑149 (MQ=255)               gTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGAt                                                                                                                                        <  2:115891/149‑1 (MQ=255)                tCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATc                                                                                                                                       <  4:217173/149‑1 (MQ=255)                  aCGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcct                                                                                                                                     <  1:103047/149‑3 (MQ=255)                  aCGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcct                                                                                                                                     <  5:229454/149‑3 (MQ=255)                  aCGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcct                                                                                                                                     >  6:229454/1‑147 (MQ=255)                      tCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTcc                                                                                                                                 >  3:391202/1‑149 (MQ=255)                               tGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcc                                                                                                                                      >  4:358346/1‑134 (MQ=255)                               tGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcc                                                                                                                                      <  3:358346/135‑2 (MQ=255)                                 gCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCtt                                                                                                                      <  4:391202/149‑1 (MQ=255)                                      tCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAAt                                                                                                                 <  4:86846/149‑1 (MQ=255)                                       cATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATa                                                                                                                >  5:279176/1‑149 (MQ=255)                                         tGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATa                                                                                                                >  2:24812/1‑147 (MQ=255)                                            cGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGcc                                                                                                           >  4:175515/1‑149 (MQ=255)                                                    aaCCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGGAATACAGCCTGGCGATc                                                                                                   >  3:181082/1‑149 (MQ=255)                                                       cACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATc                                                                                                                                       <  6:383181/110‑1 (MQ=255)                                                             ccccGCCAGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGACCCAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCACGCATGCGATCGCCGCCACCCCCAGCTTGACATACAGCCTGGCGAACTACCAGAGc                                                                                          >  8:356291/1‑149 (MQ=255)                                                              cccGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCg                                                                                         >  1:106044/1‑149 (MQ=255)                                                                            ttGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGcc                                                                            >  5:318726/1‑148 (MQ=255)                                                                                       ctgGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTg                                                                                                                     <  7:69666/96‑1 (MQ=255)                                                                                       ctgGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTg                                                                                                                     >  8:69666/1‑96 (MQ=255)                                                                                       ctgGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGAc                                                                 <  5:178078/147‑1 (MQ=255)                                                                                       ctgGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACAt                                                               <  4:280699/149‑1 (MQ=255)                                                                                           aCAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACAtgctg                                                           >  3:368764/1‑149 (MQ=255)                                                                                               cGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCGCTAAATGGACAtgatgctt                                                        >  1:135946/1‑147 (MQ=255)                                                                                                  gCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTgg                                                    <  7:152403/149‑1 (MQ=255)                                                                                                       ggTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGa                                                 <  6:318726/147‑1 (MQ=255)                                                                                                        gTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCg                                              >  5:173435/1‑149 (MQ=255)                                                                                                        gTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCg                                              >  5:95018/1‑149 (MQ=255)                                                                                                          cacaGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGtt                                            >  3:171663/1‑149 (MQ=255)                                                                                                           acaGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTc                                           <  2:106044/149‑1 (MQ=255)                                                                                                              gcgcCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTcccc                                        <  4:171663/149‑1 (MQ=255)                                                                                                                  ccGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAg                                    >  1:260994/1‑149 (MQ=255)                                                                                                                  ccGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAg                                    >  2:41672/1‑149 (MQ=255)                                                                                                                     gACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGGTTGGCGATCGTTCCCCTGAGCGa                                 >  3:332848/1‑149 (MQ=255)                                                                                                                        aaGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGAccc                              >  5:84177/1‑149 (MQ=255)                                                                                                                        aaGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGAccc                              >  7:347195/1‑149 (MQ=255)                                                                                                                          gCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCctc                            >  4:388112/1‑149 (MQ=255)                                                                                                                           cAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCctct                           <  1:24812/149‑1 (MQ=255)                                                                                                                                ggTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGTCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCaa                       <  7:44646/148‑1 (MQ=255)                                                                                                                                ggTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAg                      >  2:316195/1‑149 (MQ=255)                                                                                                                                     gtCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGa                                                                  <  4:39275/99‑1 (MQ=255)                                                                                                                                     aTCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCggg                 >  7:212602/1‑149 (MQ=255)                                                                                                                                      tCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGACTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCTTTCCCCTGAGCGACCCTCTGCAAGTCGGGc                >  2:200548/1‑149 (MQ=255)                                                                                                                                          gATCGCCCCCATGTCAACGATGACATCGCATCCACCCACAGAATGAAATACAGCCTGGCGATCTCCAACAGCGCTGCACGCCTGCCG‑AAACTCGACATCCTGCGTTAGGCGATCGATCAACTGAGAGACCCTCTGCAAGTCGGGACAgg            >  4:366370/1‑149 (MQ=255)                                                                                                                                          gATCGCATCCTTGACATGGGTGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAgg            >  5:183790/1‑149 (MQ=255)                                                                                                                                            tCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGc           >  4:353536/1‑148 (MQ=255)                                                                                                                                               cACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGa       >  6:206018/1‑149 (MQ=255)                                                                                                                                                aCCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGAc      >  1:185115/1‑149 (MQ=255)                                                                                                                                                    aTGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGCCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGCAGCTg  >  8:135295/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                      GGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGACGCTG  >  NC_002947/3762939‑3763234

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: ‑