Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,669,714	T→G	23.8%	intergenic (+38/+37)	prpD → / ← acnB	2‑methylcitrate dehydratase/aconitate hydratase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,669,714	0	T	G	23.8%	98.1 / 35.7	59	intergenic (+38/+37)	prpD/acnB	2‑methylcitrate dehydratase/aconitate hydratase B
Reads supporting (aligned to +/- strand):  ref base T (25/20);  new base G (7/7);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 7.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

GCTTTGCCCGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGATGTCTTTCG  >  NC_002947/2669573‑2669863                                                                                                                                              |                                                                                                                                                       gCTTTGCCCGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCt                                                                                                                                                    >  2:173983/1‑146 (MQ=255) gCTTTGCCCGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTGGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCt                                                                                                                                                    <  1:173983/146‑1 (MQ=255)  cTTTGCCCGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCgg                                                                                                                                               <  1:126348/150‑1 (MQ=255)        ccGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGCttt                                                                                                                                         <  2:899727/150‑1 (MQ=255)        ccGGCAGCGGTGGCAGCAGGGTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCttt                                                                                                                                         <  2:1219141/150‑1 (MQ=255)                           gTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCa                                                                                                                      >  2:688884/1‑150 (MQ=255)                                  aaCTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACg                                                                                                               >  2:832652/1‑150 (MQ=255)                                      gtgCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGGGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCTGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTg                                                                                                           >  2:723784/1‑150 (MQ=255)                                       tgCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGa                                                                                                          >  2:1179786/1‑150 (MQ=255)                                           aGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAGCAACAAAGCCCCGGCATCGCTGCCGCGGCTCTAGTGACAACCTGTAACTCAGCTTACGCCTGA‑accc                                                                                                     >  2:473448/1‑149 (MQ=255)                                           aGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCa                                                                                                                      >  2:598870/1‑134 (MQ=255)                                           aGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCa                                                                                                                      <  1:598870/134‑1 (MQ=255)                                            ggACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑accac                                                                                                    >  1:482216/1‑150 (MQ=255)                                                 agcagAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGCTTTGtt                                                                                                                                      <  2:300418/112‑1 (MQ=255)                                                 agcagAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGCTTTGtt                                                                                                                                      >  1:300418/1‑112 (MQ=255)                                                     gAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGACGGGGATTTGTTCACAATCTTTAACTCAGCTTACGCCTGA‑ACCACCGGGATCtt                                                                                           >  1:673187/1‑150 (MQ=255)                                                          tGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGt                                                                                      >  1:598111/1‑150 (MQ=255)                                                          tGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGc                                                                                                                                            <  1:909495/97‑1 (MQ=255)                                                          tGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGc                                                                                                                                            >  2:909495/1‑97 (MQ=255)                                                           ggAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGtt                                                                                                                                      <  1:685875/102‑1 (MQ=255)                                                           ggAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGtt                                                                                                                                      >  2:685875/1‑102 (MQ=255)                                                           ggAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGtt                                                                                     <  1:194801/150‑1 (MQ=255)                                                            gAAGGCACGGCTGTGCGCAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAAAACAGCTTGCGCGTGA‑ACCACCGGGCTCTTGGCGTTg                                                                                    >  2:112998/1‑150 (MQ=255)                                                                                    gTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGCACGCTGCg                                                            >  2:1170256/1‑150 (MQ=255)                                                                                       gACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCg                                                                                                                                                <  1:611378/64‑1 (MQ=255)                                                                                       gACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCg                                                                                                                                                >  2:611378/1‑64 (MQ=255)                                                                                             tttgtGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑accacc                                                                                                   <  2:1309975/102‑1 (MQ=255)                                                                                             tttgtGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑accacc                                                                                                   >  1:1309975/1‑102 (MQ=255)                                                                                             tttgtGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGCTTTGtt                                                                                                                                      >  1:843490/1‑68 (MQ=25)                                                                                             tttgtGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCAGCGATGCCGGGGCTTTGtt                                                                                                                                      <  2:843490/68‑1 (MQ=25)                                                                                               tgtgATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGaa                                                 <  2:396918/150‑1 (MQ=255)                                                                                                gtgATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGACACCGCC‑TGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAg                                                <  1:1170256/150‑1 (MQ=255)                                                                                                    tatGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTc                                                    >  2:946807/1‑142 (MQ=255)                                                                                                    tatGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTc                                                    <  1:946807/142‑1 (MQ=255)                                                                                                       gAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAg                                                >  2:1325188/1‑143 (MQ=255)                                                                                                       gAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAg                                                <  1:1325188/143‑1 (MQ=255)                                                                                                        aaGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTa                                        >  2:638812/1‑150 (MQ=255)                                                                                                                    caGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTc                            <  2:706898/150‑1 (MQ=255)                                                                                                                    caGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTc                            <  1:611352/150‑1 (MQ=255)                                                                                                                     aGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCg                           <  2:673187/150‑1 (MQ=255)                                                                                                                        cccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCtt                                                                                           >  2:1330107/1‑83 (MQ=255)                                                                                                                        cccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCtt                                                                                           <  1:1330107/83‑1 (MQ=255)                                                                                                                         ccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCa                                            <  2:284503/129‑1 (MQ=255)                                                                                                                         ccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCa                                            >  1:284503/1‑129 (MQ=255)                                                                                                                         ccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCa                        >  2:930501/1‑149 (MQ=255)                                                                                                                         ccAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAg                       >  1:1125125/1‑150 (MQ=255)                                                                                                                         ccAAACAACAAAGCCCCGGCATCGCCGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCa                        <  1:930501/149‑1 (MQ=255)                                                                                                                                 caaAGCCCCGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTg               >  2:680646/1‑150 (MQ=255)                                                                                                                                  aaaGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGt              >  1:309296/1‑150 (MQ=255)                                                                                                                                  aaaGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGt              >  1:915251/1‑150 (MQ=255)                                                                                                                                  aaaGCCCCGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGATGCCGCTTcgc                                                                       >  1:87078/1‑93 (MQ=38)                                                                                                                                  aaaGCCCCGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGATGCCGCTTcgc                                                                       <  2:87078/93‑1 (MQ=38)                                                                                                                                   aaGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTc             <  2:319719/150‑1 (MQ=255)                                                                                                                                      ccccGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGAt          <  2:309296/150‑1 (MQ=255)                                                                                                                                      ccccGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGAt          >  1:939231/1‑150 (MQ=255)                                                                                                                                      ccccGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGAt          >  1:1395736/1‑150 (MQ=255)                                                                                                                                       cccGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGaa                                                 <  2:152015/110‑1 (MQ=255)                                                                                                                                       cccGGCAGCGATGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGaa                                                 >  1:152015/1‑110 (MQ=255)                                                                                                                                             aTCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGATGTCTTTc   <  2:1125125/150‑1 (MQ=255)                                                                                                                                              tCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGATGTCTTTcg  <  2:915251/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                       GCTTTGCCCGGCAGCGGTGTCAGCAGGTTTTCGAACTGTGCAAGGACCAGCAGAAGCTGGAAGGCACGGCTGTGCACAGGTTCGTGGACTTGTTTGTGATATGAAGCGGCCGGCACAGGCCCAAACAACAAAGCCCCGGCATCGCTGCCGGGGCTTTGTTTACAACCTGTAACTCAGCTTACGCCTGA‑ACCACCGGGATCTTGGCGTTGGCTGCCGCTTCGCGGAACTCGGCGATCTGGTCGAAGCTCAGGTAGCGGTAAACGTCGGCAGCCATGCTGTCGATGTCTTTCG  >  NC_002947/2669573‑2669863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑