Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,590,199	+C	100%	intergenic (‑98/‑158)	glnE ← / → RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,590,199	1	.→C	100.0%	204.6	57	intergenic (‑98/‑158)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Reads supporting (aligned to +/- strand):  new base (55/0):  ref base (0/2):  total (55/2)

CATGGCGCCAGACTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.CCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCTTGACCC  >  NC_014034/2590099‑2590293                                                                                                          |                                                                                                  cATGGCCCCAGCCTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.g.cg                                                                                                    <  1:2941169/101‑1 (MQ=255)    ggCGCCAGACTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.ccc                                                                                                <  1:1130565/101‑1 (MQ=255)    ggCGCCAGACTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.ccc                                                                                                >  2:2258353/1‑101 (MQ=255)      cgcAAGATTAGCCGCCTCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCAAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.cccc..c                                                                                            <  2:1907213/101‑1 (MQ=37)      aaccAGACTACCCGCCGAAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.cccc..c                                                                                            <  2:2670321/99‑1 (MQ=255)       gcaaGACTACCCCCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.cccc..cc                                                                                           <  2:1380444/98‑2 (MQ=255)       cccAGACTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.cccc..cc                                                                                           <  1:2198707/100‑2 (MQ=255)             cTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCggg                                                                                     >  1:4527328/1‑101 (MQ=255)              tAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGt                                                                                    >  2:219530/1‑101 (MQ=255)                  cgccgcAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGcc                                                                                >  2:4629873/1‑101 (MQ=255)                     cgcagccccgGGGTAAGGGCGCGAAACTCCCCCGCCCCTGTCATCTTGGCGCAAATACCCGGGGGGGGGGGGGGG..GCG.GCCC.CCCC..CG.CCGGGTCGCCTCg                                                                             <  2:640366/95‑1 (MQ=255)                     cgcAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCg                                                                             >  2:2969302/1‑101 (MQ=255)                       cAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGgc                                                                           >  1:4419767/1‑101 (MQ=255)                         aGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGgcgc                                                                         >  1:2337075/1‑101 (MQ=255)                         aGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGGGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGCCCCCTCGgggc                                                                         >  1:58335/1‑101 (MQ=37)                          gCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCACGGCGCa                                                                        >  1:1816951/1‑101 (MQ=255)                           ccccGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCaa                                                                       >  2:532790/1‑101 (MQ=255)                           ccccGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCaa                                                                       >  1:4210064/1‑101 (MQ=255)                             ccGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGc                                                                     >  1:2804157/1‑101 (MQ=255)                             ccGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGc                                                                     >  1:1321063/1‑101 (MQ=255)                              cGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGcc                                                                    >  1:1863345/1‑101 (MQ=255)                                ggTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGa                                                                  >  2:406463/1‑101 (MQ=255)                                  tCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAgg                                                                >  1:2692696/1‑101 (MQ=255)                                   cAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGc                                                               >  1:2784106/1‑101 (MQ=255)                                     aGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGa                                                             >  2:2235189/1‑101 (MQ=255)                                         gcgcAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAAtc                                                         >  1:111970/1‑101 (MQ=255)                                          cgcAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAAtct                                                        >  2:4023847/1‑101 (MQ=255)                                              aaTGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAAtctcttc                                                    >  1:1105549/1‑99 (MQ=255)                                              aaTGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTcc                                                    >  1:4066487/1‑101 (MQ=255)                                                tGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGCGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATTTATcccc                                                  >  1:1187875/1‑101 (MQ=37)                                                ccgcccgttccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTcccc                                                  >  2:3609640/10‑101 (MQ=37)                                                 gccccgccccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCg                                                 >  2:2627227/1‑101 (MQ=255)                                                 gccccgccccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCg                                                 >  2:4252544/1‑101 (MQ=255)                                                 gccccgccccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCCCGGCGCCAGCCGGGGCGAAAACTCTccccc                                                 >  2:3187565/1‑100 (MQ=37)                                                   ccccccccTGGCCTCTTGGCCGCAATCCCCCGGGGGGGGGGGGGGCCCCC.C.CC.CCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGa                                                <  2:3790672/101‑1 (MQ=12)                                                      gccccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGAcccc                                            >  1:3263039/1‑101 (MQ=255)                                                       ccccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATATCTCCCCGACCCCt                                           >  2:2298772/1‑101 (MQ=255)                                                         ccTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTg                                         >  1:1092345/1‑101 (MQ=255)                                                           tGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTgcg                                       >  2:3258323/1‑101 (MQ=255)                                                            gTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTgcgg                                      >  1:1914110/1‑101 (MQ=255)                                                              cATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTgcggcg                                    >  2:4665724/1‑101 (MQ=255)                                                              cATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCCACCCCCTgcggcg                                    >  1:4060095/1‑101 (MQ=37)                                                                tCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCa                                  >  2:3359767/1‑101 (MQ=255)                                                                 cTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCaa                                 >  2:1127179/1‑101 (MQ=255)                                                                   tGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTACCCGACCCCCTGCGGCGCAGTg                               >  1:4371667/1‑101 (MQ=37)                                                                    ggCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGt                              >  1:2955703/1‑101 (MQ=255)                                                                     gcgcGAATATCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTa                             >  2:2740222/1‑101 (MQ=255)                                                                           atatCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGGCATGTAAAAATc                       >  2:3994236/1‑101 (MQ=37)                                                                            tatCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTACAAATCt                      >  2:3869303/1‑101 (MQ=255)                                                                            tatCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCt                      >  1:1810301/1‑101 (MQ=255)                                                                             atCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCtt                     >  2:1254114/1‑101 (MQ=255)                                                                             atCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCtt                     >  1:4171893/1‑101 (MQ=255)                                                                              tCCCGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCttt                    >  1:1333970/1‑101 (MQ=255)                                                                              gccgggggggGGGGGGGG..GCG.GCCC.CCCC..CC.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCttt                    <  2:804335/97‑1 (MQ=37)                                                                               ccgggggggGGGGGGGG..GCC.C.CC.CCCC..CGCCCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTc                   <  1:2264475/98‑1 (MQ=37)                                                                               cccGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTc                   >  2:3566535/1‑101 (MQ=255)                                                                                ccGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTca                  >  1:4262917/1‑101 (MQ=255)                                                                                ccGGGGGGTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTATCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTca                  >  2:2289042/1‑101 (MQ=255)                                                                                 gggggggTGGGGGGG..GGC.G.CC.CCCCCGCG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTca                  <  2:720183/100‑1 (MQ=25)                                                                                 ggggcggTGGGGGGG..GCACC.CC.CCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTcac                 <  2:2757835/100‑1 (MQ=37)                                                                                  ggggggTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCCACCCCTTGCGGCGCAATGGAAAAAGCTTTcaca                >  1:4025771/1‑101 (MQ=37)                                                                                   gggggTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGGAAAAATCTTTCACAt               >  1:3711437/1‑101 (MQ=255)                                                                                       gTGCGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATcccc           >  1:4276074/1‑101 (MQ=255)                                                                                        tGCGGGGG..GCT.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCct          >  2:988423/1‑101 (MQ=255)                                                                                          cGGGGG..GCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCctct        >  1:3878553/1‑101 (MQ=255)                                                                                           ggggg..gCC.G.CCCCCCC..CGCCCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCctct        <  2:2264495/101‑1 (MQ=38)                                                                                           ggggg..gCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCtt       >  2:1385167/1‑101 (MQ=255)                                                                                           ggggg..gCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGAACCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCtt       >  2:2960488/1‑101 (MQ=255)                                                                                            gggg..gCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGCGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCTTg      >  2:1816848/1‑101 (MQ=255)                                                                                                  gCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCTTgaccc  >  2:2934074/1‑101 (MQ=255)                                                                                                  gCA.G.CGCCCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCTTgaccc  >  2:220287/1‑101 (MQ=255)                                                                                                          |                                                                                                  CATGGCGCCAGACTAGCCGCCGCAAGCCCCGGGTCAAGGCGCGCAAATGCCCCGCCCCTGTCATCTTGGCGCGAATATCCCGGGGGGTGCGGGGG..GCA.G.CG.CCCC..CG.CCGGGTCGCCTCGGCGCAAGCCGAGGCGAAATCTCTCCCCGACCCCTTGCGGCGCAATGTAAAAATCTTTCACATCCCCTCTTGACCC  >  NC_014034/2590099‑2590293 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 22 ≤  ATCG  < 32 ≤  ATCG  < 40 ≤  ATCG