Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,185,930	+C	91.4%	intergenic (+203/‑302)	mtlK → / → RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,185,930	1	.→C	91.4%	3.5 ‑1.4 ‑0.2	35	intergenic (+203/‑302)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
Reads supporting (aligned to +/- strand):  new base (15/17):  ref base (0/3):  total (15/20)
Fisher's exact test strand distribution p-value = 2.44e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 6.06e-01

GCTCCG.CCCCGCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGA.ACCG.CCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGCCCGCCGGGTCTC  >  NC_014034/2185836‑2185988                                                                                                  |                                                            gCTCCGCCCCCGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCG.CCC.Cctt                                                     <  2:763092/101‑1 (MQ=37)   tccgcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCG.CCC.Cctttc                                                   <  1:4211526/96‑3 (MQ=37)    ccgcccccGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCa                                                   <  1:3818167/97‑1 (MQ=37)       gcccccgcgcccccGGCGTATTTCTCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCAAAAGAAACGCCGA.GCCGCCCC.CTTTCAcc                                                 <  1:4063879/92‑1 (MQ=255)             gcacccccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCt                                           <  1:74305/98‑1 (MQ=38)             gcacccccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCACCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCt                                           >  2:33043/4‑101 (MQ=255)              cacccccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTc                                          <  2:1691676/99‑1 (MQ=39)                cccccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCaa                                        >  2:69951/1‑101 (MQ=255)                  cccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAat                                      <  1:1406787/101‑1 (MQ=255)                   ccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAata                                     >  2:3229616/1‑101 (MQ=255)                   ccGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAata                                     <  1:3834752/101‑1 (MQ=255)                    cgacGTATTGATCCAAAGAAACACCCGCGGCTTGCTCCGTAGACCTTG.TTTTGATGGCGCAAGAAACGCCTA.CCCT.CCCTCTTTCCCCTTGGCTCAAatat                                    <  2:1928571/98‑1 (MQ=255)                      gCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATcc                                  >  2:2365467/1‑101 (MQ=255)                      gCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATcc                                  >  2:3922031/1‑101 (MQ=255)                        gTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCg                                >  1:2431908/1‑101 (MQ=255)                         tATTTATCCCAAGGAAAAGCAGCGGCTTGCCCCGAAAGACGTG.ATTTGATGGGAGAAGAAACACCGA.ACCGACGC.CTTTCAACCTTGATCAAATATGCCgg                               >  2:1507383/1‑101 (MQ=255)                            ttATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGC.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCTggggg                            >  2:2839074/1‑101 (MQ=255)                             tATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCCAATATCCCGGGGGt                           >  1:3550084/1‑101 (MQ=255)                              aTCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTc                          <  2:3053969/101‑1 (MQ=255)                               tCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTcc                         <  1:3797515/101‑1 (MQ=255)                               tCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTcc                         <  1:2956496/101‑1 (MQ=255)                                cccAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCg                        <  1:2502815/101‑1 (MQ=255)                                  cAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCggg                      <  1:114148/101‑1 (MQ=255)                                   aaGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCgggg                     >  1:959075/1‑101 (MQ=255)                                   aaGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCgcgg                     <  1:2419760/101‑1 (MQ=255)                                     gAAAAAGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGc                   >  2:3914541/1‑101 (MQ=255)                                      aaaaaGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCg                  <  1:3792130/101‑1 (MQ=255)                                       aaaaGCAGCGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCgg                 >  1:445142/1‑101 (MQ=255)                                          agcagcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGc              <  1:1406507/101‑1 (MQ=255)                                           gcagcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGcc             >  2:3208555/1‑101 (MQ=255)                                           gcagcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGcc             >  2:3610289/1‑101 (MQ=255)                                           gcagcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTATCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAgac             >  2:4206718/1‑99 (MQ=37)                                             agcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGcccc           <  1:3234756/101‑2 (MQ=37)                                              gcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGccccc          <  2:958990/101‑3 (MQ=37)                                              gcGGCTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGccccc          <  2:3454461/101‑3 (MQ=37)                                              gcGGCTTCCCCCGAAGGCTTTG.TTTTGATGGCAAAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGccccc          <  2:1504252/101‑3 (MQ=25)                                                  cTTGCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGA.ACCGCCCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGcccccggcg      >  2:401625/1‑95 (MQ=25)                                                      cccgGAGGGCCTTG.TTTTGACGGCACAAGAAACGCCGACCCCC.CCC.CTTTCCCCTTGGCTCAAATTCCCCGGGGGTCGGGGGGGGGAGcccccggcgggtc  <  2:1067302/101‑11 (MQ=9)                                                                                                  |                                                            GCTCCG.CCCCGCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTTGCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGA.ACCG.CCC.CTTTCACCTTGGCTCAAATATCCCGGGGGTCCGGGGGCGGAGCCCGCCGGGTCTC  >  NC_014034/2185836‑2185988 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG