Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	16,945	T→C	7.8%	T119T (ACT→ACC)	PP_5421 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	16,945	0	T	C	7.8%	140.8 / 2.8	51	T119T (ACT→ACC)	PP_5421	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base C (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CAGGTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCTGCTC  >  NC_002947/16805‑17092                                                                                                                                             |                                                                                                                                                    cAGGTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGt                                                                                                                                              >  2:167144/1‑148 (MQ=255) cAGGTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCAGTGATCACCGAAAAGt                                                                                                                                              >  3:284433/1‑148 (MQ=255)    gTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAAt                                                                                                                                          >  2:224508/1‑149 (MQ=255)    gTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCAGTGATCACCGAAAAGTTacg                                                                                                                                          <  4:284433/149‑3 (MQ=255)           tCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCTGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACt                                                                                                                                                     >  6:192572/1‑131 (MQ=255)           tCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCTGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACt                                                                                                                                                     <  5:192572/131‑1 (MQ=255)             gcgGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGaaaa                                                                                                                                                <  1:139616/134‑1 (MQ=255)                    ggCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCt                                                                                                                           <  3:13429/148‑1 (MQ=255)                     gcgcGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTgg                                                                                                                         >  6:201234/1‑149 (MQ=255)                     gcgcGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTgg                                                                                                                         <  6:147401/149‑1 (MQ=255)                                  tttGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAg                                                                                                            <  5:201234/149‑1 (MQ=255)                                     gaagtgaagCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGaa                                                                                                          <  2:227014/148‑1 (MQ=255)                                      aagtgaagCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCt                                                                                                                       >  3:120781/1‑134 (MQ=255)                                      aagtgaagCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCt                                                                                                                       <  4:120781/134‑1 (MQ=255)                                            agCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGAt                                                                                                   <  1:167144/148‑1 (MQ=255)                                             gCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCt                                                                                                                           >  7:268494/1‑123 (MQ=255)                                             gCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCt                                                                                                                           <  8:268494/123‑1 (MQ=255)                                               cTCACAACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTAt                                                                                               >  8:162009/1‑149 (MQ=255)                                                tCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTAt                                                                                               >  2:114731/1‑148 (MQ=255)                                                      ccgacTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGgc                                                                                        <  7:7555/149‑1 (MQ=255)                                                               gATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCag                                                                               <  3:290949/149‑1 (MQ=255)                                                                     cAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCAc                                                                                            >  2:190741/1‑130 (MQ=255)                                                                     cAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCAc                                                                                            <  1:190741/130‑1 (MQ=255)                                                                        cGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGc                                                                      <  2:290909/149‑1 (MQ=255)                                                                            aGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCAt                                                                    >  3:240729/1‑147 (MQ=255)                                                                              gCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAgg                                                                >  1:221694/1‑149 (MQ=255)                                                                                 gCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGt                                                             >  3:22836/1‑149 (MQ=255)                                                                                  cGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGtt                                                            <  1:224508/149‑1 (MQ=255)                                                                                           gCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGAt                                                                                                   >  2:190531/1‑101 (MQ=255)                                                                                           gCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGAt                                                                                                   <  1:190531/101‑1 (MQ=255)                                                                                             cGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTaa                                                 <  7:260693/149‑1 (MQ=255)                                                                                              gCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAg                                                                                                         <  1:113486/92‑1 (MQ=255)                                                                                              gCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAg                                                                                                         >  2:113486/1‑92 (MQ=255)                                                                                               cTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATg                                               <  1:339736/149‑1 (MQ=255)                                                                                                  aGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGc                                             <  4:97626/148‑1 (MQ=255)                                                                                                   gcgcTACTTCCCCGCCACTGCCCGTAACTGTTCGGTGAGCACTGAAAAGTTAATTGAAGCTGCACCCCAGGCTACCACTCTTAGAAGGCTGAGGTATCACCGGCGCGGTCCAGAGCATTCGCATCAGCCGTGTGAGGAGGTAATGGCGa                                           >  6:278780/1‑149 (MQ=255)                                                                                                       tACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGATGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTATCGCATCAGGccct                                                            >  4:39732/1‑125 (MQ=255)                                                                                                          ttCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCaa                                    >  2:4659/1‑149 (MQ=255)                                                                                                          ttCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGAGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCaa                                    >  2:357519/1‑149 (MQ=255)                                                                                                          ttCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATAACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCaa                                    >  7:315244/1‑149 (MQ=255)                                                                                                          ttCAACGCCACTGCCCGTAACTTTTCGGTGATCACCGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCaa                                    >  5:73721/1‑149 (MQ=255)                                                                                                                      gCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGgccgcc                        >  1:223618/1‑149 (MQ=255)                                                                                                                       cccGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGgccgcc                        >  7:294994/1‑148 (MQ=255)                                                                                                                       cccGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGgccgc                         <  7:162009/147‑1 (MQ=255)                                                                                                                         cGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTAt                     <  2:223618/149‑1 (MQ=255)                                                                                                                          gTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTc                                                                        <  5:178145/97‑1 (MQ=255)                                                                                                                          gTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTc                                                                        >  6:178145/1‑97 (MQ=255)                                                                                                                                  tCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTg             <  1:4659/148‑1 (MQ=255)                                                                                                                                      tGATCACCGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGAt        <  6:73721/149‑1 (MQ=255)                                                                                                                                        aTCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGAGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATc       <  1:357519/148‑1 (MQ=255)                                                                                                                                          cACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCGGCCTATGACCGTTGCAGATCTGc    >  4:12823/1‑149 (MQ=255)                                                                                                                                            cTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAAt                               <  4:36269/120‑1 (MQ=255)                                                                                                                                            cTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAAt                               >  3:36269/1‑120 (MQ=255)                                                                                                                                             tGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCt      >  1:136508/1‑144 (MQ=255)                                                                                                                                             tGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCt      <  2:136508/144‑1 (MQ=255)                                                                                                                                             tGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCTGctc  >  1:329230/1‑148 (MQ=255)                                                                                                                                             tGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCTGctc  >  5:268615/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                                    CAGGTTTTCCTCGCGGATGGGCGCGAGTGGTGGTTTGAAGTGAAGCCTCACGACCGACTGAAGATTGCCAGCGTCAGGCAGCGACTGGATGCCGCTGAGCGCTACTTCAACGCCACTGCCCGTAACTTTTCGGTGATCACTGAAAAGTTAATTGAAGCTGAACCCCTGGCTACCAATCTTAGAAGGCTGATGTATCACCGGCGCGGTCCAGAGCTTTCGCATCAGGCGTTGGAGGAGGTAATGGCGACCTTCAACGAATGGCCGCCTATGACCGTTGCAGATCTGCTC  >  NC_002947/16805‑17092

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: ‑