Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,049,913	C→T	9.3%	intergenic (+46/‑55)	quiA → / → oprB‑III	quinate dehydrogenase/carbohydrate‑selective porin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,049,913	0	C	T	9.3%	113.0 / 3.0	45	intergenic (+46/‑55)	quiA/oprB‑III	quinate dehydrogenase/carbohydrate‑selective porin
Reads supporting (aligned to +/- strand):  ref base C (19/20);  new base T (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

TCGCCGAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCGCAGCACC  >  NC_002947/4049769‑4050060                                                                                                                                                  |                                                                                                                                                      tcGCCGAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTg                                                                                                                                                     >  5:116322/1‑147 (MQ=255)   gCCGAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGt                                                                                                                                                    <  5:140863/146‑1 (MQ=255)    ccGAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGa                                                                                                                                                >  8:151924/1‑149 (MQ=255)      gAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGc                                                                                                                                              <  1:96096/149‑1 (MQ=255)        aGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCgg                                                                                                                                            <  7:227768/149‑1 (MQ=255)           ccGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTATAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAG‑GGGCCTTGTAGGAGCGGGCt                                                                                                                                         <  3:93060/149‑1 (MQ=255)            cGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCtt                                                                                                                                        <  1:69207/149‑1 (MQ=255)              gCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTACTACAA‑GGCCCCAGTAGGAGCGGGGTTGc                                                                                                                                      >  4:64218/1‑149 (MQ=255)                  gCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGGAAGCCCGCGCCGAAAA‑AGGCCCGGTAGGTGCGGGGGTGG‑‑Ccgc                                                                                                                                >  1:130603/1‑149 (MQ=255)                   cAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑Ccgcg                                                                                                                               <  3:154652/149‑1 (MQ=255)                         gtggtgATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGcccc                                                                                                                                                       >  4:44836/1‑121 (MQ=255)                         gtggtgATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGcccc                                                                                                                                                       <  3:44836/121‑1 (MQ=255)                                  aCTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAgc                                                                                                                >  8:230888/1‑148 (MQ=255)                                    tgctgGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAG‑GGGCCTTGTAGGAGCgg                                                                                                                                            <  8:247787/121‑1 (MQ=255)                                    tgctgGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAG‑GGGCCTTGTAGGAGCgg                                                                                                                                            >  7:247787/1‑121 (MQ=255)                                      ctgGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGACCGCACCTAGAA‑GGGCCCGGGAGGTGCGGGGGTTC‑‑CCGCGGCTGGCCCGCAAATAAAAc                                                                                                            >  5:198848/1‑149 (MQ=255)                                                                  tGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAAtt                                                                                <  7:295621/149‑1 (MQ=255)                                                                      gACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTACTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGc                                                                             >  1:209188/1‑148 (MQ=255)                                                                           tgtgATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCAc                                                                        <  6:116322/148‑1 (MQ=255)                                                                           tgtcATTTTTAACGCGCTCCCGAAAAACGGCGGCGCCTGGTTCGGGGCAAACCCCGCTCCAACAC‑GGCCCGTGTCGTTGGGGGGTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCAc                                                                        <  5:215554/148‑1 (MQ=255)                                                                             tgATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCCAGCCCCCGCCGAAAA‑AGCCCCGGTAGGAGCGGGCGTGG‑‑CCCCGCATGGCCCGCAAATGCCACCCGACATTATGTTATTGCCGCCGCAATTGGCCTCAcccc                                                                     >  4:67214/1‑149 (MQ=255)                                                                              gATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCACCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCgaga                                                                                                      >  5:68063/1‑115 (MQ=255)                                                                              gATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCACCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCgaga                                                                                                      <  6:68063/115‑1 (MQ=255)                                                                                tttCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCGAAAA‑GGCCCCGGTAGGAGCCGGCTTGC‑‑CCGCGAATGCCCCGCAAAGACAACCCGAGATTATGTAATGCCAGACGCAAATCGCATCAccccccc                                                                  >  5:118675/1‑147 (MQ=255)                                                                                  tCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCAcc                                                                 <  3:64218/148‑1 (MQ=255)                                                                                   cTTACCCTCGCCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCAACAA‑GGCCCCTGTCGGCGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCAccc                                                                <  6:198573/148‑1 (MQ=39)                                                                                      aCGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCGGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCctgct                                                            >  5:96407/1‑149 (MQ=255)                                                                                        gCTCTGCCGAAAAACCGCGTCGCTGGCTGCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCGGAAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCctgctgc                                                          <  2:175337/149‑1 (MQ=39)                                                                                           ctGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAAGGGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCctgctgctg                                                        >  1:244262/1‑149 (MQ=255)                                                                                                   aaaCCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTGCTACAA‑GGCCCCTGTAGGAGCGGGCGTGCGACCGCGAATGCCCCTCAAAGCCAACCCGAGATTGTGTAATGCCATCCGCAATTGGCATCACCCCCACCCTGCGGctggccctgg                                                 >  1:260695/1‑149 (MQ=255)                                                                                                               cTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGcc                                   <  2:244262/149‑1 (MQ=255)                                                                                                                     cgcgTGCAAGCCCGCTCCTACAA‑GGCCCGTGTAGGAGCTGGCTTGC‑‑CCGCTAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGc                              <  6:198848/148‑1 (MQ=255)                                                                                                                     cgcgGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTg                               <  2:209188/147‑1 (MQ=255)                                                                                                                      gcgGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCa                            <  4:274727/149‑1 (MQ=255)                                                                                                                       cgGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAg                           <  6:137686/149‑1 (MQ=255)                                                                                                                          gCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGcga                        >  7:161743/1‑149 (MQ=255)                                                                                                                            aaGCCCGCTCCTACAA‑GGCCCCTGTCGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGcgacg                      <  6:118675/149‑1 (MQ=255)                                                                                                                              gCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGAt                    >  8:134503/1‑149 (MQ=255)                                                                                                                               cccGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGc                                                                             >  8:269327/1‑91 (MQ=255)                                                                                                                               cccGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGc                                                                             <  7:269327/91‑1 (MQ=255)                                                                                                                                ccGCTCCTACAG‑GGGCCTTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGAtct                  >  1:321288/1‑149 (MQ=255)                                                                                                                                ccGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGAtct                  <  7:186272/149‑1 (MQ=255)                                                                                                                                      caaaaa‑GCCCCCTTTTGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGAc            <  5:206981/145‑1 (MQ=255)                                                                                                                                      cTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGa             <  3:155589/148‑1 (MQ=255)                                                                                                                                      cTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGAc            >  1:60161/1‑149 (MQ=255)                                                                                                                                             ggCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCgcag      >  2:103429/1‑149 (MQ=255)                                                                                                                                              gCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCgcag      >  8:159068/1‑148 (MQ=255)                                                                                                                                                 ccTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCGCAGCAcc  >  1:296732/1‑149 (MQ=255)                                                                                                                                                 ccTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCGCAGCAcc  >  3:118569/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                      TCGCCGAAGACCGGCAAGCAGTACGTGGTGATCACTGCTGGCGGCGCCCGCCAGTCGACTGACCGTGGCGACTATGTGATTTCTTACGCTCTGCCGTAAAACCGCGTCGCCTGCTTCGCGGGCAAGCCCGCTCCTACAA‑GGCCCCTGTAGGAGCGGGCTTGC‑‑CCGCGAATGCCCCTCAAAGACAACCCGAGATTCTGTAATGCCATCCGCAATTCGCATCACCCCCACCCTGCTGCTGGCCCTGGCCAGCACCACTGCCCTTGCCAGCGACGATCTCATGACCCGCAGCACC  >  NC_002947/4049769‑4050060

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: ‑