Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,995,659	+A	4.8%	intergenic (+199/+21)	RCAP_rcc02802 → / ← RCAP_rcc02803	membrane dipeptidase/hypothetical protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,995,659	2	.→A	4.8%	6.0 0.0 ‑0.3	63	intergenic (+199/+21)	RCAP_rcc02802/RCAP_rcc02803	membrane dipeptidase/hypothetical protein
Reads supporting (aligned to +/- strand):  new base (3/0):  ref base (49/11):  total (52/11)
Fisher's exact test strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 5.30e-01

CGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAATT  >  NC_014034/2995562‑2995759                                                                                                      |                                                                                                      cgccCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGACGCCCCGGCttttc                                                                                                     >  2:2815451/1‑98 (MQ=255)       gCACCCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCg                                                                                             <  2:2877615/101‑1 (MQ=255)              gTCGGCGGCCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCCGCTT..GCCGGGGGGAAATccc                                                                                      >  1:987598/1‑101 (MQ=255)                 ggcggcCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGGGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCg                                                                                   >  1:4607369/1‑101 (MQ=255)                    ggcCCGGCCCCCTGCTTTCCTGTGC.AAAAATCGG.CGGGGGGGTGCGGGGGGGGGGCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTc                                                                                <  2:4436225/101‑1 (MQ=16)                      cccAGCGCCCT.CTTTTCCTTGGACAAAATGCG.CGGGGGGGTGGGGGGGGGGGGCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAg                                                                              <  2:403594/101‑1 (MQ=25)                       ccAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGt                                                                             >  2:1417389/1‑101 (MQ=255)                          cggctttgtttttCCTTGG.AAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAgc                                                                             >  2:2260547/10‑100 (MQ=0)                            gcCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGGCGCCCCGGCTT..GCCCGGGCGAAATCCCCCGCCCAATCCCag                                                                        >  2:1915329/1‑101 (MQ=18)                                 gtttttCCTTGG.AAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttcat                                                                      >  1:1058553/3‑96 (MQ=0)                                   ttttCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACttt                                                                 >  1:2991227/1‑101 (MQ=255)                                    tttCCTGGG.CAAGAGACG.GCGGGGGGGGGGGGGGGGGCGGGCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTc                                                                <  1:1362820/101‑1 (MQ=25)                                     ttCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGGCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCCGTCCCCCAGACTTTCg                                                               >  1:2053905/1‑101 (MQ=21)                                      tCCTTGG.AAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttcatcttca                                                                 >  2:3659601/1‑91 (MQ=0)                                         ctggaaaaaaTCCG.GGGGGGGGGGGGGGGGGCGGTCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGAcc                                                            <  1:3123620/95‑1 (MQ=25)                                           gg.CAAAATACG.CCGGGGGGTGCGGGGGGCAGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCg                                                         >  1:4528715/1‑101 (MQ=255)                                                 aaTACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGATCAGTCCCCGAGACTTTCACCCTCGAACCg                                                    >  2:1088520/1‑101 (MQ=25)                                                   tACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGCCGCCCCGGCCT..GGCGGGGCGAAAACCCCCGCTCAGTCCCCGAGACTTTCGACCTCGAACCggg                                                  >  1:3081407/1‑101 (MQ=37)                                                            ggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGAcgc                                          >  1:596885/1‑101 (MQ=255)                                                             gggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGAcgcg                                         >  1:1300790/1‑101 (MQ=255)                                                               gTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGCCGCCGa                                       >  2:952220/1‑101 (MQ=255)                                                                 gCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATg                                     >  1:1771106/1‑101 (MQ=255)                                                                 gCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATg                                     <  1:199170/101‑1 (MQ=255)                                                                 gCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCACAGAATTTCGACCTCGAACCGGGGCAGACGCGGATg                                     >  2:602670/1‑101 (MQ=255)                                                                  cGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAATCCCAGAGACTTTCGACCTCGCACCCGGCCCGACGCGGATgc                                    >  2:2518057/1‑101 (MQ=38)                                                                   ggggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgcg                                   >  2:3504661/1‑101 (MQ=255)                                                                   ggggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgcg                                   >  2:3420874/1‑101 (MQ=255)                                                                   ggggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgcg                                   >  1:3097920/1‑101 (MQ=255)                                                                   ggggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGGCAGACGCGGATgcg                                   >  1:1270322/1‑101 (MQ=255)                                                                    gggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgcgc                                  >  2:3386575/1‑101 (MQ=255)                                                                    gggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGGCAGACGCGGATgcgc                                  >  2:392222/1‑101 (MQ=255)                                                                       ggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAgg                               <  1:333612/101‑1 (MQ=255)                                                                       ggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAgg                               >  1:2403843/1‑101 (MQ=255)                                                                        gCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGc                              >  2:3670598/1‑101 (MQ=255)                                                                         cGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCg                             >  1:3492674/1‑101 (MQ=255)                                                                          ggccccccccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCgg                            <  1:2518231/97‑1 (MQ=255)                                                                          ggAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCgg                            >  1:2275589/1‑101 (MQ=255)                                                                          ggAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCgg                            >  2:3372982/1‑101 (MQ=255)                                                                           gAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCggg                           >  2:3109753/1‑101 (MQ=255)                                                                           gAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCggg                           >  1:143844/1‑101 (MQ=255)                                                                           gAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCggg                           >  2:1258319/1‑101 (MQ=255)                                                                            aGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGc                          >  2:3306607/1‑101 (MQ=255)                                                                            aGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGc                          >  2:4376988/1‑101 (MQ=255)                                                                             gCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGTGcc                         >  1:722063/1‑101 (MQ=255)                                                                             gCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCCCAGTCCCAGAGACTTTCGACCTCGAACCGGGGCAGACGCGGATGGGCAGGCGGGcc                         >  1:884355/1‑101 (MQ=255)                                                                                ccccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCATAGACTTTCGACCTCGAACCGGGCCAGACGCGGATGCGCAGGCGGGCCGaa                      >  2:4589351/1‑101 (MQ=255)                                                                                 ccgg.cgGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGaaa                     <  2:2403038/98‑1 (MQ=255)                                                                                 cccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGaaa                     >  2:1984235/1‑101 (MQ=255)                                                                                  ccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAg                    >  2:3390873/1‑101 (MQ=255)                                                                                   cg.cgGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGc                   >  1:1944243/1‑101 (MQ=255)                                                                                   cg.cgGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGc                   >  1:3197355/1‑101 (MQ=255)                                                                                      cgGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCg                 >  2:4258746/1‑101 (MQ=255)                                                                                       gggTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGc                >  2:3815812/1‑101 (MQ=255)                                                                                       gggTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCCCAAGCCGc                >  2:3278915/1‑101 (MQ=255)                                                                                        ggTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCa               <  2:3668349/101‑1 (MQ=255)                                                                                        ggTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCa               >  1:1369421/1‑101 (MQ=255)                                                                                         gTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCaa              >  1:4260701/1‑101 (MQ=255)                                                                                          tCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAg             <  1:2815667/101‑1 (MQ=255)                                                                                           cGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAgg            >  2:4661810/1‑101 (MQ=255)                                                                                            gcaccGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGc           >  1:2656614/4‑101 (MQ=255)                                                                                             ccccGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCt          >  2:3635483/1‑101 (MQ=255)                                                                                             ccccGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCt          >  1:3160357/1‑101 (MQ=255)                                                                                              cccGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTg         >  2:4304256/1‑101 (MQ=255)                                                                                               ccGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCGgg        >  2:3091148/1‑101 (MQ=255)                                                                                                 ggCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCg      >  1:3936322/1‑101 (MQ=255)                                                                                                  gCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGa     >  2:3649390/1‑101 (MQ=255)                                                                                                   cTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGaa    >  1:4202829/1‑101 (MQ=255)                                                                                                    tt..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAAt   >  1:1500237/1‑101 (MQ=255)                                                                                                    tt..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAAt   <  1:4259034/101‑1 (MQ=255)                                                                                                    tt..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAAt   <  1:1088609/101‑1 (MQ=255)                                                                                                     t..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAAtt  <  2:2990998/101‑1 (MQ=255)                                                                                                      |                                                                                                      CGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGG.CAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAAAGCCGCAAGGCTGGCGAATT  >  NC_014034/2995562‑2995759 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 22 ≤  ATCG  < 31 ≤  ATCG  < 39 ≤  ATCG