Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,763,083	C→T	14.8%	T109I (ACC→ATC)	PP_3326 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,763,083	0	C	T	14.8%	131.7 / 12.3	54	T109I (ACC→ATC)	PP_3326	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (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 = 2.83e-01

CCGGGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGAC  >  NC_002947/3762936‑3763230                                                                                                                                                    |                                                                                                                                                     ccGGGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCAc                                                                                                                                                      >  4:176600/1‑148 (MQ=255) ccGGGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCAc                                                                                                                                                      <  3:176600/148‑1 (MQ=255)    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                                                                                                                                 >  6:229454/1‑147 (MQ=255)                     aCGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcct                                                                                                                                 <  5:229454/149‑3 (MQ=255)                     aCGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCATCCTTGACATGGGTGCGATcct                                                                                                                                 <  1:103047/149‑3 (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)                                                                                                                                                    |                                                                                                                                                     CCGGGAACATGATCCCGGTCACGGTCGAGCGCCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAAGGATGCGATCGCCTCCACCCACAGCTTGAAATACAGCCTGGCGATCTACCAGAGCGGTGCACGCCTGCCG‑AAACTGGACATGCTGCGTTTGGCGATCGTTCCCCTGAGCGACCCTCTGCAAGTCGGGCCAGGCAAGAC  >  NC_002947/3762936‑3763230

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: ‑