Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,732,696	+C	88.5%	intergenic (‑120/‑283)	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	1,732,696	1	.→C	88.5%	14.0 ‑0.6 ‑0.1	52	intergenic (‑120/‑283)	RCAP_rcc01601/tgt	FeS assembly SUF system protein/queuine tRNA‑ribosyltransferase
Reads supporting (aligned to +/- strand):  new base (5/41):  ref base (1/5):  total (6/46)
Fisher's exact test strand distribution p-value = 5.40e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 7.45e-01

CTAGAGTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.CCGGGC..GGGCG..G..G..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGCCGCATGCC  >  NC_014034/1732596‑1732780                                                                                                        |                                                                                             cTAGAGTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.a                                                                                               >  2:3636574/1‑101 (MQ=255)   agagTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGGGGC.G.C.cc                                                                                            >  1:1852744/1‑101 (MQ=255)    gagTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.ccc                                                                                           <  2:564748/101‑2 (MQ=255)     agTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.cccg                                                                                          <  1:1152385/101‑3 (MQ=255)     agTTTATATAGGATATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.G.cccg                                                                                          >  1:2423198/1‑99 (MQ=255)      gTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.Cccgg                                                                                         <  1:3636827/101‑1 (MQ=255)        ttATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.ccccggg                                                                                       >  1:463732/1‑96 (MQ=255)        ttATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.Cccgggc                                                                                       <  2:3876443/101‑3 (MQ=255)        ttATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.Cccgggc                                                                                       <  1:732344/101‑3 (MQ=255)        ttATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.Cccgggc                                                                                       <  1:3562931/101‑3 (MQ=255)         tatataGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGCGG.C.Ccgggc..g                                                                                     >  2:1975609/1‑101 (MQ=255)         tatataGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.ccccgggg                                                                                      >  1:379918/1‑95 (MQ=255)          atataGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.C.Cccggg..ggg                                                                                   >  1:3309749/1‑101 (MQ=255)           tataGGGTATCGGGGGGAGAGGTAAAGTCCGTCTGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..ggg                                                                                   <  1:1246910/101‑1 (MQ=255)            ataGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..gggg                                                                                  <  1:3068853/101‑2 (MQ=255)             taGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.GCC.Ccgggc..ggggg                                                                                 <  1:2416650/101‑3 (MQ=255)              aGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..gggggc                                                                                <  2:29253/101‑4 (MQ=255)                ggTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..gggggctc                                                                              <  2:2125867/101‑6 (MQ=255)                ggTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..gggggctc                                                                              <  2:1343894/101‑6 (MQ=255)                 gTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGGCGCGGC.G.G.CCCCGG..GGGGg..g..g..ggg                                                                      >  1:3211375/1‑99 (MQ=255)                  tATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCcgggc..gggggctccg                                                                            <  1:3123120/101‑8 (MQ=39)                   aTCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGCGG.C.CCGGGC..GGGGg..g..g..gggc                                                                     >  1:3565799/1‑98 (MQ=255)                   aTCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.CC.CGC..GGCCg..g..g..gggacc                                                                   >  2:3482098/1‑96 (MQ=255)                    tCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.CCCGGG..GGGGg..g..g..gggccc                                                                   >  2:3258430/1‑96 (MQ=255)                     cGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.Cccggg..ggggg..g..gcgggcac                                                                    >  2:4404700/1‑94 (MQ=255)                      ggggggAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGG..GGGGG..G..G..Gcgcccc                                                                  >  1:2144327/1‑100 (MQ=255)                             gagGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.AGCCGGGC..CGGGG..G..G..GCGCCGGCCccccc                                                           >  2:3598854/1‑101 (MQ=255)                              agGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGC..GGGGG..G..G..GCGCCCCCCcccccc                                                          >  1:1317387/1‑100 (MQ=255)                               ggTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCAccccc                                                           <  2:4112580/101‑1 (MQ=25)                                gTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCg                                                          <  2:4150718/101‑1 (MQ=25)                                gTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCg                                                          <  1:1866188/101‑1 (MQ=25)                                 tAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCgg                                                         <  2:2123651/101‑1 (MQ=25)                                 tAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGC..AGG.G..G..G..CCCCCCGCCccggctcccc                                                      >  2:2207937/1‑93 (MQ=255)                                  aaaGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGG..GGGGG..G..G..GCCCCCCCCcccccccccc                                                      >  2:2846371/1‑96 (MQ=255)                                  aaaGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGC..GGGGGATC..C..GCCCCCGCACCCCCGGc                                                        <  1:3049891/101‑1 (MQ=37)                                  aaaGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGC..GGGGG..G..G..CCGCCCCCCcccccccccc                                                      >  2:452225/1‑96 (MQ=255)                                   aaGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCg                                                       <  1:2230478/101‑1 (MQ=25)                                    aGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGt                                                      <  2:2039214/101‑1 (MQ=25)                                     ggCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTa                                                     <  1:4291833/101‑1 (MQ=25)                                      gCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTAt                                                    <  1:2822342/101‑1 (MQ=25)                                        cGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTAttt                                                  <  2:2197933/101‑1 (MQ=25)                                              tGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCa                                            <  1:3599102/101‑1 (MQ=21)                                                 ggggCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCaaga                                         <  2:4033100/101‑1 (MQ=21)                                                  gggCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCaagaa                                        <  2:937029/101‑1 (MQ=21)                                                   ggCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCaagaag                                       <  2:2109448/101‑1 (MQ=18)                                                   ggCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCaagaag                                       <  2:1852620/101‑1 (MQ=18)                                                     cGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAgaagaa                                     <  1:2161466/101‑1 (MQ=18)                                                      ggAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGaaa                                    <  2:1299150/101‑1 (MQ=18)                                                       gAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAAc                                   <  2:2078712/101‑1 (MQ=18)                                                         aaGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACaa                                 <  1:3469757/101‑1 (MQ=18)                                                         aaGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACaa                                 <  1:3918651/101‑1 (MQ=18)                                                         aaGCCGCGTGACAAGCAGGGTTTCGCCGCGGCGGGGCAGCGGC.G.ACCCGGGCAGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACaa                                 <  2:1058920/101‑1 (MQ=18)                                                           gCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGc                               <  1:3525803/101‑1 (MQ=18)                                                           gCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGc                               <  2:463680/101‑1 (MQ=18)                                                                gTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGAc                          <  2:3214114/101‑1 (MQ=18)                                                                 tGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGAcc                         <  1:2781204/101‑1 (MQ=18)                                                                  gCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCa                        <  1:3881522/101‑1 (MQ=18)                                                                          gggTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGcccccc                <  2:2977817/101‑1 (MQ=18)                                                                           ggTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCt               <  2:2144188/101‑1 (MQ=18)                                                                           ggTTTCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCt               <  2:3015952/101‑1 (MQ=18)                                                                             tttCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGc             <  2:1831561/101‑1 (MQ=18)                                                                              ttCGCCGCGGCGGGGCCGCGGC.G.ACCCGGGC..GGGGT..GTCC..GCCGCCACGCCCCTGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCa            <  2:3696035/101‑1 (MQ=25)                                                                              ctccccgcTGCGGGGCCGCCGC.G.ACCCGGGCGGGGGCC..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCa            <  2:2006285/97‑1 (MQ=21)                                                                                 gccgcGGCGGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGcc         <  2:667191/101‑1 (MQ=18)                                                                                    gcggggGGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGCCGCa      <  2:1317290/101‑1 (MQ=18)                                                                                     cggcggGGCCGCGGC.G.ACCCGGGG..GGGGG..G..GCCGCCCCCCCCCCCCCCGCGGATTTTCGCCCAGAAGAAACAAACGGGGCCAAGCCCCCCCCCACCCGccg     >  2:2082861/1‑99 (MQ=255)                                                                                      ggcggGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGCCGCATg    <  1:3258662/101‑1 (MQ=18)                                                                                        cggGGCCGCGGC.G.ACCCGGGCGGGGGCT..C..C..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGCCGCATGcc  <  1:298500/101‑1 (MQ=18)                                                                                                        |                                                                                             CTAGAGTTTATATAGGGTATCGGGGGGAGAGGTAAAGGCCGTCGGTGCGGGGCGGAAAGCCGCGTGCCAAGCAGGGTTTCGCCGCGGCGGGGCCGCGGC.G.A.CCGGGC..GGGCG..G..G..GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAACAAGCGGGACCAGGCCCCCCTGCAGCCGCATGCC  >  NC_014034/1732596‑1732780 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 38 ≤  ATCG