Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,732,860	G→C	18.3%	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	18.3%	2.8 ‑2.7 0.0	36	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 (12/17):  total (12/24)
Fisher's exact test strand distribution p-value = 7.04e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

CCCCCCTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GT...C....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGC  >  NC_014034/1732761‑1732948                                                                                                     |                                                                                                        gcccccCGCAGCCGCATGCCGTCCGCGTCAACATGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..c                                                                                                      <  2:2290234/100‑1 (MQ=255)  cccccTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..cc                                                                                                     <  2:3474848/101‑1 (MQ=255)  cccccTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG..cg                                                                                                     >  2:1747849/1‑100 (MQ=255)      cTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..cccccc                                                                                                 <  2:852805/101‑1 (MQ=255)      cTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..cccccc                                                                                                 >  1:2041480/1‑101 (MQ=255)        acAGCCGCATGCCGTCCGCGTGAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG..GCGCCC....gc                                                                                           >  1:2639940/2‑100 (MQ=255)         cAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGACCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....gcg                                                                                          >  2:3573503/1‑99 (MQ=255)            ccGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....gcgggt                                                                                       <  1:788266/101‑6 (MQ=255)             cGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGC.GGGGGTGGAG..CCCCCC....gcggggcg                                                                                     >  2:1249094/1‑94 (MQ=255)               cATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG..gcccccccggggggg                                                                                        >  2:4429586/1‑92 (MQ=255)               cATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGGAG..gccccccccgggggc                                                                                        >  2:562252/1‑92 (MQ=255)               cATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGAAG..CCCCCC....gcggggcgc                                                                                    >  2:1663018/1‑93 (MQ=255)                              aaCAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTGCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGa                                                                 <  1:3070274/101‑1 (MQ=21)                                   gCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.Ga                                                           <  1:3828337/101‑1 (MQ=21)                                   gCAAGGCCCCTGTTTTTCCCAGGGAAAATT.CCCCTTTTTTTTTTTGGGGGGGGGGGGGGGGGGCCC..CCCCCC....GG...CGGGTCGCCGCGGGCTTGCCCGAGGC.g                                                            <  2:2473163/101‑1 (MQ=2)                                     aaGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GCGGGT....CGCCTCGGGCTTGCCCGAGGC.Gaaa                                                         <  2:625536/101‑1 (MQ=18)                                      agacccctGCTTTTCCTAGGAAAATGC.CGCCCTTTTTTC.TTTCGGGGGGGGCGGGGGTAAAG..CCCCCCCGCGGG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAg                                                        <  2:2041340/97‑1 (MQ=2)                                           cccGTTTTTCCCAGGCAAAATG.CGCCCTTCTTTCTTTTGGGGGGGGGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcc                                                   <  1:2131675/101‑1 (MQ=17)                                           cccGCTTTTCCTAGGCAAAATC.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcc                                                   <  1:2819242/101‑1 (MQ=18)                                              gCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTccccc                                                <  1:612871/101‑1 (MQ=21)                                               cTTTTCCTAGGCAAAATC.CGCCCTGCTTTCTTTGCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcccccc                                               <  2:2216636/101‑1 (MQ=17)                                                    ccTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaa                                          <  2:3038981/101‑1 (MQ=21)                                                      tAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaaa                                        <  1:4631361/101‑1 (MQ=21)                                                      tAGCCAAAATC.CGCCTTTTTTTCTTTGGGGGGGGGCGGGGGGTAAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaaa                                        <  1:1388593/101‑1 (MQ=9)                                                      caagCAAAATCCCGCCTTTTTTTCTTTGGGGGGGGGGGGGGGGTAACC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaa                                         <  2:4139376/98‑1 (MQ=2)                                                        ggCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAAcc                                      <  1:2228877/101‑1 (MQ=21)                                                         gaaaagTA.CCCCCTTCTTTCTTTCGGGGGGGGCGGGGGGTGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCt                                     <  2:2568441/99‑1 (MQ=17)                                                             aaTA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGAAGGCCCCCCCG...GG...G....GGCCTCGGGGTTGGCCGCGGCGGGAGGCTCCCCCCCCTGAAAActcgcc                                  >  2:3650040/1‑96 (MQ=255)                                                              aTA.CGCCCTTCTTTCTTTTGGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCt                                <  2:4638946/101‑1 (MQ=18)                                                               atccGCCTTGCTTTCTTTGGGGGGGGGGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCt                                <  2:4515289/98‑1 (MQ=9)                                                                tccGCCTTTTTTTCTTTTGGGGGGGGGGGGGGGTGAGC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTg                               <  1:1265839/99‑1 (MQ=12)                                                                     ccTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTgcgcgc                          <  2:2866880/101‑1 (MQ=21)                                                                       ttctttttTTTGGGGGGGGGGGGGGGTAAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGt                        <  1:2787169/101‑1 (MQ=18)                                                                                 tggggggggGGGGGGGGGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt              <  1:1178798/99‑1 (MQ=18)                                                                                 gggggggggGGGGGGGTGACG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt              <  1:4502018/99‑1 (MQ=18)                                                                                  ggggggggGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt.t            <  1:2841421/100‑1 (MQ=18)                                                                                   gggggggGGGGGGGGGACG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt.tt           <  1:331732/101‑1 (MQ=18)                                                                                           ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGGCTGCGCGCGTCGGTTTCCCT.TTCGCCCCgg   >  2:1558645/1‑101 (MQ=18)                                                                                           ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCCGccccg   >  1:4429828/1‑99 (MQ=21)                                                                                           ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCCTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCgg   >  1:1171363/1‑101 (MQ=21)                                                                                           ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCCTGAAAACCTTGCCTGCGCGCGGCGCTTTCCCT.TTCGGccccg   >  2:3513571/1‑99 (MQ=18)                                                                                           ggggggTGAAG..CCCCCCGCG.GG...G....CGCCCCGGGCTTGCCCCCGGG.GGAAACTTCCCCCCGCGAAAAACCTGCCCGCGCGCGCCGCCTTCCCTCTTCGCCCCg    >  1:3965202/1‑101 (MQ=255)                                                                                            gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCggg  >  2:1492929/1‑100 (MQ=21)                                                                                            gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGgc  >  2:2282214/1‑101 (MQ=21)                                                                                            gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGgc  >  2:1473257/1‑101 (MQ=21)                                                                                                     |                                                                                                        CCCCCCTGCAGCCGCATGCCGTCCGCGTCAACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GT...C....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGC  >  NC_014034/1732761‑1732948 Base quality scores:  ATCG  < 3 ≤  ATCG  < 8 ≤  ATCG  < 20 ≤  ATCG  < 31 ≤  ATCG  < 39 ≤  ATCG