Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,384,075	T→C	7.5%	intergenic (‑10/+109)	PP_2985 ← / ← PP_5548	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,384,075	0	T	C	7.5%	147.7 / 2.9	53	intergenic (‑10/+109)	PP_2985/PP_5548	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (25/24);  new base C (2/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

CCCTGGGACAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGACCGTC  >  NC_002947/3383928‑3384217                                                                                                                                                    |                                                                                                                                                 cccTGGGACAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCtt                                                                                                                                                 <  4:136296/149‑1 (MQ=255)  ccTGGGACAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTg                                                                                                                                                <  1:218240/149‑1 (MQ=255)   cTGGGAAAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGATATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTgg                                                                                                                                               >  8:220581/1‑149 (MQ=255)       gACAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGa                                                                                                                                            >  3:160755/1‑148 (MQ=255)            aCGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAact                                                                                                                                       >  8:320751/1‑148 (MQ=255)             cGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAactac                                                                                                                                     <  8:241840/149‑1 (MQ=255)               tGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGTGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACtt                                                                                                                                   <  7:320751/149‑1 (MQ=255)                                aTAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTc                                                                                                                   >  6:73342/1‑148 (MQ=255)                                    cAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATc                                                                                                               >  2:227251/1‑148 (MQ=255)                                            tCAGCGTCGAATGCCGATGCTATGAGTGGCTTGGCTGTGAGGAAGCGGGCGGGCCATGTGGGATCCTAGGGGGTACTCTTGCTGGTCAGTGCCATGTCAGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCAATCAAGGCgtgt                                                                                                      <  2:233924/149‑1 (MQ=255)                                            tCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCgtg                                                                                                       <  5:73342/148‑1 (MQ=255)                                                  tCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGGCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCAttt                                                                                                >  5:104626/1‑149 (MQ=255)                                                  tCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCAttt                                                                                                <  7:220581/149‑1 (MQ=255)                                                   cGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTg                                                                                               >  2:240079/1‑149 (MQ=255)                                                    gAATGCCGAGGCTATGAGCGGCTTCCCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGCGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCAttt                                                                                                <  2:221066/147‑1 (MQ=255)                                                         tagAGGATATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGTGATAGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCAttt                                                                                                <  4:183182/140‑1 (MQ=255)                                                         ccGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTgagatcg                                                                                         >  3:183182/1‑143 (MQ=255)                                                          cGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGa                                                                                      >  3:247409/1‑149 (MQ=255)                                                           gAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGAc                                                                                     <  4:247409/149‑1 (MQ=255)                                                                  tGAGTGGGTGGTCTGTCCGGCAGCGTGCGGGCCATGTGGGATGGCAGGGGGTAAGCTTGCTGGGCAGTGCCATGTCCGTTCCTTGTCGATCACTACTTGAGGCGCCGGATTGTCCATCAAGGGGTGTGCATTTGCCA‑‑CCGACTTagag                                                                               <  4:44711/148‑1 (MQ=255)                                                                       ggCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGTGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCgt                                                                                                        <  7:70978/120‑1 (MQ=255)                                                                       ggCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCgt                                                                                                        >  8:70978/1‑120 (MQ=255)                                                                             tctgtcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGt                                                                   >  3:359947/1‑149 (MQ=255)                                                                               tgtcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCg                                                                 >  4:82804/1‑149 (MQ=255)                                                                                gtcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATc                                                                        >  8:275628/1‑141 (MQ=255)                                                                                gtcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATc                                                                        <  7:275628/141‑1 (MQ=255)                                                                                 tcAGTAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGa                                                                                      <  8:280533/126‑1 (MQ=255)                                                                                 tcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGcc                                                               <  4:160755/149‑1 (MQ=255)                                                                                 tcAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGcc                                                               <  4:359947/149‑1 (MQ=255)                                                                                 tcAGAAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGa                                                                                      >  7:280533/1‑126 (MQ=255)                                                                                          gggcgggcCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGAtgtg                                                       >  2:280969/1‑148 (MQ=255)                                                                                                                 ggggTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCACGCCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCa                                 <  1:280969/149‑1 (MQ=255)                                                                                                                    gTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCtt                            <  1:227251/149‑1 (MQ=255)                                                                                                                    gTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCtt                            <  6:158534/149‑1 (MQ=255)                                                                                                                                gTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCa                 >  4:80276/1‑148 (MQ=255)                                                                                                                                 tCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGt                                                                   >  7:196462/1‑97 (MQ=255)                                                                                                                                 tCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGt                                                                   <  8:196462/97‑1 (MQ=255)                                                                                                                                   aGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTcc                                                                                                                  >  1:327759/1‑50 (MQ=255)                                                                                                                                   aGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTcc                                                                                                                  <  2:327759/50‑1 (MQ=255)                                                                                                                                   aGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATc             >  5:88823/1‑149 (MQ=255)                                                                                                                                    gTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCg            <  6:88823/149‑1 (MQ=255)                                                                                                                                     tGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACTCTCGCATATCGa           <  6:104626/149‑1 (MQ=255)                                                                                                                                       ccATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGa           >  4:17544/1‑147 (MQ=255)                                                                                                                                       ccATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGa           >  2:228050/1‑147 (MQ=255)                                                                                                                                       ccATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCAGGATTGTCCATCAAGGCGAGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACAATCGCATATCGATa         >  7:258225/1‑149 (MQ=255)                                                                                                                                       ccATGTCCGTTCCCTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCg                                          >  5:81136/1‑116 (MQ=255)                                                                                                                                       ccATGTCCGTTCCCTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCg                                          <  6:75946/116‑1 (MQ=255)                                                                                                                                       ccATGTCCGTTCCCTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCg                                          >  5:75946/1‑116 (MQ=255)                                                                                                                                       ccATGTCCGTTCCCTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCg                                          <  6:81136/116‑1 (MQ=255)                                                                                                                                           gTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTCGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGAcc     >  3:331796/1‑149 (MQ=255)                                                                                                                                            tCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGACCg    <  3:17544/149‑1 (MQ=255)                                                                                                                                             ccGTTCCTTGGCGATAACTACTTGAGGCGCCGTATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGACCGt   >  1:42236/1‑149 (MQ=255)                                                                                                                                              ctgtCCTTTGCGATAAGTACTTGAGGCGGCTGATTGTACATCAAGGCGTGTGGATTTGCCA‑‑CCGACTTACAGGGCTATCAGTGTCGGAGAGATGTGTCTTCGGAATCCGGTCGATTCACGCTTCATCACTCGCATATCGATAGACCGTc  <  8:258225/146‑1 (MQ=255)                                                                                                                                              cGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGACCGTc  >  2:145463/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                 CCCTGGGACAGACGTGCTTCCAACGTGGTGGATAGCAATCAGTTCAGCGTCGAATGCCGAGGCTATGAGTGGCTTGTCTGTCAGGAAGCGGGCGGGCCATGTGGGATCGTAGGGGGTAATCTTGCTGGTCAGTGCCATGTCCGTTCCTTGGCGATAACTACTTGAGGCGCCGGATTGTCCATCAAGGCGTGTGCATTTGCCA‑‑CCGACTTACAGGGCAATCACTGTCGCCGAGATGTGTCTTCGGAATCCGGGCGATTCACGCTTCAACACTCGCATATCGATAGACCGTC  >  NC_002947/3383928‑3384217

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑