Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,732,860	G→C	24.2%	intergenic (‑284/‑119)	RCAP_rcc01601 ← / → tgt	FeS assembly SUF system protein/queuine tRNA‑ribosyltransferase

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	1,732,860	0	G→C	24.2%	2.9 ‑2.0 0.0	27	intergenic (‑284/‑119)	RCAP_rcc01601/tgt	FeS assembly SUF system protein/queuine tRNA‑ribosyltransferase
Reads supporting (aligned to +/- strand):  new base (0/7):  ref base (7/13):  total (7/20)
Fisher's exact test strand distribution p-value = 1.37e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

GCCCCCCTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...GT...C....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGCCCGGC  >  NC_014034/1732760‑1732948                                                                                                       |                                                                                                          gCCCCCCTGCAGCCGCATGCCATCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAg                                                                                                           >  1:2401826/1‑101 (MQ=255)  ccccccTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...c                                                                                                       <  2:3693148/101‑1 (MQ=255)   cccccTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...cc                                                                                                      >  1:792538/1‑101 (MQ=255)      ccggCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...ccccc                                                                                                   <  1:904965/98‑1 (MQ=255)       cTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGGG...cccccc                                                                                                  >  1:300995/1‑101 (MQ=255)         gCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...gc                                                                                             <  1:345728/101‑2 (MQ=255)          cAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG...caccccccc                                                                                               >  2:1156469/1‑98 (MQ=255)           aGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG...CGCCCC...gccg                                                                                           >  2:57291/1‑98 (MQ=255)             ccGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG...gccccccccggg                                                                                            >  2:2571934/1‑95 (MQ=255)               gCATGCCGCCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...gcgggtcg                                                                                       <  2:1699102/101‑8 (MQ=255)                 aTGCCGTCCGGGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...gcgggtcgcc                                                                                     <  2:3460540/101‑10 (MQ=38)                               aaCAGGCAAGGCCCCCG.TTTTTCCTAGGC.AAAATCCGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGa                                                                 <  2:2401650/101‑1 (MQ=18)                                  ggggcaGGGCCCCG.TTTTTCCCTAGC.AAAAACCCCCCTTTTTTTTTTTGGGGGGGGGGGGGGGGGAAG...CCCCCC...CG...CGGGTCG..CCTCGGGCTTGCCCGAgg                                                               <  1:3802626/96‑1 (MQ=2)                                  aggccgggcccccG.CTTTCCATGGAA.AAAATGC.CCCTTTTTTTTTTGCGGGGGGGGGGGGGGATAAA...CCCCCC...GG...CGGGTCG..CCTCGGGCTTGCCCGAGGc                                                              <  2:2330100/92‑1 (MQ=2)                                      aaGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCTTTTTTTCTTTGGGGGGGGGCGGGGGGGGAAC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.Gaaa                                                         <  2:970752/101‑1 (MQ=9)                                      aaGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGTGGGGGGTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.Gaaa                                                         <  1:3505702/101‑1 (MQ=18)                                          gCCCCGTCTTTCCCTGGGA.AAAATCCCCCTTTCTTTTTTTGGGGGGGGGGGGGGGGGGACG...CCCCCC...GCGGGT....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCt                                                      <  2:368073/101‑1 (MQ=2)                                          gCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTGCGGGGGGGGGGGGGGTGAAG...CCCCCC...GCGGGT....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCtt                                                     <  2:3313039/101‑1 (MQ=18)                                             ccG.CTTTCCCAAGGA.AAAATCCGCCTTTCTTTCTTTGGGGGGGGGCGGGGGGTGAAG...CCCCCC...GCGGGT....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.ccc                                                 <  1:1283984/101‑1 (MQ=2)                                              cccgttttCCTAAGCAAAAATCCCCCTTTTTTTTTTTTGGGGGGGGCGGGGGGTGAAC...CCCCCC...GC...GGGT.CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.cc                                                  <  2:359166/97‑1 (MQ=2)                                              cG.CTTTTCCTAGGC.AAAATACCCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...GC...GGGT.CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.cccc                                                <  2:1617701/101‑1 (MQ=18)                                                  ttttCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCg                                             <  2:2785093/101‑1 (MQ=21)                                                     tCCTAGGC.AAAATCCGCCCTTCTTTCTTTTCGGGGGGGGGGGGGGTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGa                                          <  1:3103737/101‑1 (MQ=18)                                                       cTAGGA.AAAATCCGCCCTTTTTTCTTTCGGGGGGGGCGGGGGGTGAAC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGaaa                                        <  2:329583/101‑1 (MQ=9)                                                          tac.AAAAAGCGCCGTTTTGTCTTTGGGGGGGGGGGGGGGGGGAAC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAAcc                                     <  1:1310269/99‑1 (MQ=2)                                                                 aTACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGAAGGCCCCCCCCG..GG...C....GG..CCCCGGGCTTCCCCGGGGG.GGAACTTT.CCCCCCCGCAAAACCTTCcc                                >  2:3522820/1‑101 (MQ=255)                                                                  tACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGAAGGC.CCCCCCG..GG...G....CG..CCCCCGGCGTGGCCCAGGCGGAAAGCTTCCCCCCCGTGaaacctgccct                                >  2:3430024/1‑93 (MQ=255)                                                                             ttctttTCGGGGGGGCGGGGGGGGGAGAC.CCCCCC...GG...G....GGGCCCCCGGGCTGGCCCGGGGG.GAAAGCTC.CCCCCCCGGAAAAAC.TGCCCGCGCGCGGCGcg                   >  2:2540037/1‑100 (MQ=255)                                                                              tttttgggggggggGGGGGGGTGACC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCtt                  <  1:3167391/94‑1 (MQ=17)                                                                                 tttCGGGGGGGCGGGGGGTGAGG...CCCCCCGCGGG...T....CG..GCCCAGGCCTGCCCCGGGC.GAAAGAGT.CCCCCCCCGAAAACCCCCCCCCCGGGCGTCGCCTTcc               >  2:91638/1‑101 (MQ=255)                                                                                      ggggggCGGGGGGGGACC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTc          <  1:341857/101‑1 (MQ=18)                                                                                        ggggGGGGGGGTGAAC...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCgg        <  1:3523073/101‑1 (MQ=21)                                                                                           gCGGGGGGTGAAG...CCCCCCGCGGG...G....CG..CCTCGGGCCTGCCCGAGGC.GAAAGCCT.TCCCCCCTGCAAAACTTGCCCGCGCGCGTCGCTTTTCCTTTCGGccc     >  2:2788887/1‑101 (MQ=12)                                                                                            cGGGGGGTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGGGAAAACCTTCCCTCCCCCCGCCCCTTTCCCTTTCGCCCCg    >  1:4034232/1‑101 (MQ=9)                                                                                            cGGGGGGTGAAG...CCCCCCGCGGG...G....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCCTCGCTTTCCCTTTCGGCCCg    >  2:4157530/1‑101 (MQ=21)                                                                                             ggggggTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGCCCgg   >  2:3048376/1‑101 (MQ=21)                                                                                             ggggggTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGCCCgg   >  1:3420310/1‑101 (MQ=21)                                                                                             ggggggTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAACTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGccccg   >  1:3548913/1‑99 (MQ=21)                                                                                              gggggTGAAG...CCCCCCGCGGG...T....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGCCCGgc  <  2:3477174/101‑1 (MQ=21)                                                                                                       |                                                                                                          GCCCCCCTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCG.CTTTTCCTAGGC.AAAATACGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG...CCCCCC...GT...C....CG..CCTCGGGCTTGCCCGAGGC.GAAAGCTT.CCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTCGGCCCGGC  >  NC_014034/1732760‑1732948 Base quality scores:  ATCG  < 3 ≤  ATCG  < 8 ≤  ATCG  < 20 ≤  ATCG  < 32 ≤  ATCG  < 40 ≤  ATCG