Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,065,253	G→C	7.8%	D65H (GAT→CAT)	PP_2677 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,065,253	0	G	C	7.8%	154.9 / 5.0	51	D65H (GAT→CAT)	PP_2677	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/21);  new base C (2/2);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01

CCTGGGCCGCCCAGGCTGCGACACAAGGCACCCACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGTTGTCGATC  >  NC_002947/3065107‑3065396                                                                                                                                                   |                                                                                                                                                ccggggCCGCCCAGGCGGCGACACAAGGCACCCACACAAACCCCGTGCCTTGCGTGATGTGGGACTTATACCACAAGCAGTTGCTGGGGCAGGCGGCGTTGGTGTTGGATGTCCGTGTGAAGCTTCTGGCGCCGCCCGTTGCCGAgggt                                                                                                                                               >  8:98475/4‑147 (MQ=255) ccTGGGCCGCCCAGGCTGCGACACAAGGCACCCACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCAAAAGCAGTTGCTGGGGCAGGCGGCGGTCGTGTTCGATGACCGTGTGAAGATTCTGGCGCCGACCTTTGCCGAGGAt                                                                                                                                               >  8:304833/1‑149 (MQ=255)                     acacAAGGCACCCACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGga                                                                                                                           <  3:224510/149‑1 (MQ=255)                                ccACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGga                                                                                                                           >  5:87491/1‑138 (MQ=255)                                ccACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGga                                                                                                                           <  6:87491/138‑1 (MQ=255)                                ccACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGccc                                                                                                                >  6:281843/1‑149 (MQ=255)                                    acaGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGc                                                                                                            >  3:187464/1‑149 (MQ=255)                                      aGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGt                                                                                                          >  1:55702/1‑149 (MQ=255)                                      aGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGt                                                                                                          <  2:55702/149‑1 (MQ=255)                                             gTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACggg                                                                                                   <  7:98475/149‑1 (MQ=255)                                                 cTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCa                                                                                                                                       <  8:193313/109‑1 (MQ=255)                                                 cTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCa                                                                                                                                       >  7:193313/1‑109 (MQ=255)                                                  ttCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTg                                                                                                                             >  4:215355/1‑118 (MQ=255)                                                  ttCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTg                                                                                                                             <  3:215355/118‑1 (MQ=255)                                                              ggACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTa                                                                                  >  6:300109/1‑149 (MQ=255)                                                                  ttCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGc                                                                              >  7:301166/1‑149 (MQ=255)                                                                     tACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTg                                                                           >  1:277348/1‑149 (MQ=255)                                                                        cacaAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTggg                                                                         >  6:148749/1‑148 (MQ=255)                                                                         acaAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTggg                                                                         >  6:214396/1‑147 (MQ=255)                                                                           aaGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCaga                                                                     <  2:277348/149‑1 (MQ=255)                                                                                gTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTg                                                                 >  1:107764/1‑148 (MQ=255)                                                                                     tGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTATCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCct                                                           >  2:117424/1‑149 (MQ=255)                                                                                     tGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGACCCct                                                           >  7:285862/1‑149 (MQ=255)                                                                                       gggCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCctc                                                          <  5:148749/148‑1 (MQ=255)                                                                                                  gTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCAtc                                               >  2:184542/1‑148 (MQ=255)                                                                                                  gTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTCGGCAGAGCTGAACCCTCTGCCGCGCAtc                                               <  1:184542/148‑1 (MQ=255)                                                                                                    tCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCAtcgt                                             >  1:194443/1‑148 (MQ=255)                                                                                                    tCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCAtcgt                                             <  2:194443/148‑1 (MQ=255)                                                                                                       tgtTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCAtcgtc                                            >  2:273971/1‑146 (MQ=255)                                                                                                       tgtTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCAtcgtc                                            <  1:273971/146‑1 (MQ=255)                                                                                                         ttCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACt                                        <  5:214396/148‑1 (MQ=255)                                                                                                            gATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACttt                                      >  1:316760/1‑147 (MQ=255)                                                                                                                 ccGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGTGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCg                               <  7:304833/149‑1 (MQ=255)                                                                                                                 ccGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCg                               <  8:301166/149‑1 (MQ=255)                                                                                                                     gtgAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGt                             >  7:306106/1‑147 (MQ=255)                                                                                                                      tgAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCTGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAg                          >  5:334352/1‑149 (MQ=255)                                                                                                                      tgAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGa                           <  2:316760/148‑1 (MQ=255)                                                                                                                        aaGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGCACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAgcg                        >  4:223858/1‑149 (MQ=255)                                                                                                                        aaGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAgc                         <  5:300109/148‑1 (MQ=255)                                                                                                                          gCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCcg                                                     <  8:27710/118‑1 (MQ=255)                                                                                                                          gCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCcg                                                     >  7:27710/1‑118 (MQ=255)                                                                                                                           cTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCgt                     <  4:187464/149‑1 (MQ=255)                                                                                                                                   gccgccCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGCGAGCGCGTGTTGCCCt             >  3:109463/1‑149 (MQ=255)                                                                                                                                    ccgccCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTg            >  3:179908/1‑149 (MQ=255)                                                                                                                                     cgccCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTgg           <  2:107764/149‑1 (MQ=255)                                                                                                                                      gccCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGt          <  4:200888/149‑1 (MQ=255)                                                                                                                                      gccCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGt          >  4:74715/1‑149 (MQ=255)                                                                                                                                          cctGCCGTGCATCCTCGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCctc                                                          <  4:250368/95‑1 (MQ=255)                                                                                                                                          cctGCCGTGCATCCTCGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCctc                                                          >  3:250368/3‑97 (MQ=255)                                                                                                                                            tGCCGTGCATCCTCGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGtt         <  6:296689/144‑1 (MQ=255)                                                                                                                                            tGCCGTGCATCCTCGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGtt         >  5:296689/1‑144 (MQ=255)                                                                                                                                              ccGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGTTGTCGatc  <  3:74715/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                CCTGGGCCGCCCAGGCTGCGACACAAGGCACCCACACAGACCCGGTGCCTTCCGTGATGTGGGACTTCTACCACAAGCAGTTGCTGGGGCAGGCGGCGTTCGTGTTCGATGACCGTGTGAAGCTTCTGGCGCCGCCCTTTGCCGAGGATGCACGGCAGGTACCGCTGGAGATCGACGCCCGGGCGTTCACGGGCGATGTGGTGCGGATTATCGCCTGGGCAGAGCTGAACCCTCTGCCGCGCATCGTCGACTTTCAGCCCGGTGAGCGCGTGTTGCCCTGGTTGTCGATC  >  NC_002947/3065107‑3065396

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: ‑