Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,481,041	T→G	100%	M329M (ATG→CTG)	RCAP_rcc02306 ←	LysM domain‑containing protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,481,041	0	T→G	100.0%	236.9	63	M329M (ATG→CTG)	RCAP_rcc02306	LysM domain‑containing protein
Reads supporting (aligned to +/- strand):  new base (58/5):  ref base (0/0):  total (58/5)

CGGCGGCGGCGGGCGGCGGCGGCGGGGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCCCATCAAGGCGCATCGCATGCGGCCCGGGCGTCTCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAGGC  >  NC_014034/2480945‑2481137                                                                                                 |                                                                                                 cggcggcggcgggcggcggcggcgggGGGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCCCCCGGCCCGCGGCCCCGAGCGCATCAAGGcgcagcgca                                                                                              >  2:4292499/1‑101 (MQ=255)      gcggcgggcggcggcggcgggGCGGCGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCgg                                                                                         <  1:4292816/101‑1 (MQ=255)            ggcggcggcggcgggGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCggg                                                                                   >  2:3764589/1‑101 (MQ=255)              cggcggcggcgggGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCg                                                                                 >  2:373659/1‑101 (MQ=255)               ggcggcggcgggGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGt                                                                                >  1:3275999/1‑101 (MQ=255)                  ggcggcgggGCGACGCCCCCGAAGCCCCGCTCCGCGCGGGGCAGCACCCGGCCCGCGGCATCCAGCGCATCAAGGCGCAGCGCACGCGGCCCGGGCGtcgc                                                                             >  2:4354777/1‑99 (MQ=255)                      gcgggGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCcgcg                                                                         >  2:4011579/1‑101 (MQ=255)                         gggCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTTGCCCCGGGc                                                                      >  2:3318854/1‑101 (MQ=255)                           gCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGGCGCCGCGGGcgc                                                                    >  1:911873/1‑99 (MQ=255)                                 cccTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGccg                                                              >  2:4974251/1‑99 (MQ=255)                                 cccTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAg                                                              >  1:4547746/1‑101 (MQ=255)                                   cTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCg                                                            >  1:100696/1‑101 (MQ=255)                                     cGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCggg                                                          >  2:4560020/1‑99 (MQ=255)                                     cGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCgcg                                                          >  1:2425368/1‑99 (MQ=255)                                     cGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTg                                                          >  1:1957145/1‑101 (MQ=255)                                      gAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGa                                                         >  1:2470752/1‑101 (MQ=255)                                      gAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGa                                                         >  2:590136/1‑101 (MQ=255)                                      gAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGa                                                         <  2:4547426/101‑1 (MQ=255)                                      gAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGa                                                         >  1:2016635/1‑101 (MQ=255)                                      gAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGa                                                         >  1:4284056/1‑101 (MQ=255)                                         gCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAAc                                                      >  1:2290659/1‑101 (MQ=255)                                          cccTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAAcc                                                     >  1:1626336/1‑101 (MQ=255)                                           ccTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAAccc                                                    >  2:1766496/1‑100 (MQ=255)                                            cTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAAccgc                                                   >  1:4822242/1‑101 (MQ=255)                                              gCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAAccgccg                                                 >  2:2892094/1‑101 (MQ=255)                                               cTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGt                                                >  2:3261446/1‑101 (MQ=255)                                                 cGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTcc                                              >  1:1053627/1‑101 (MQ=255)                                                 cGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTcc                                              >  2:2567965/1‑101 (MQ=255)                                                 cGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTcc                                              >  1:2632233/1‑101 (MQ=255)                                                  ggCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTccc                                             >  2:3768308/1‑101 (MQ=255)                                                     gcgGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgc                                          >  2:4728919/1‑101 (MQ=255)                                                      cgGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgcc                                         >  2:616629/1‑101 (MQ=255)                                                      cgGGCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgcc                                         >  2:850816/1‑101 (MQ=255)                                                       gggCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgccc                                        >  2:1257221/1‑101 (MQ=255)                                                       gggCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgccc                                        >  2:3471255/1‑101 (MQ=255)                                                       gggCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgccc                                        >  1:2489459/1‑101 (MQ=255)                                                        ggCCAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCcccgcccg                                       <  2:4821915/101‑1 (MQ=255)                                                          ccAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCcgcccgcc                                     >  2:4688022/1‑101 (MQ=255)                                                          ccAGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGAACGGCATGCGGCCCGGCCGTCGCCCCGGGCAGGCGCGCCCCGAAACCCCCGTGcccgccccgc                                     >  2:1512982/1‑98 (MQ=255)                                                            aGCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTg                                   >  2:4073104/1‑101 (MQ=255)                                                             gcccccGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCCCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGc                                  <  2:2489285/98‑1 (MQ=255)                                                             gCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGc                                  >  2:1193183/1‑101 (MQ=255)                                                             gCACCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGc                                  >  1:4799692/1‑101 (MQ=255)                                                               aCCCGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGGCCCCGCCCGCCTGCAc                                >  2:39312/1‑101 (MQ=255)                                                                 ccGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCa                              >  1:1710459/1‑101 (MQ=255)                                                                  cGGCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGGGAAACCGCCGTCCCCGCCCGCCTGCACCac                             >  2:1733007/1‑100 (MQ=255)                                                                    gCCCGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAAcc                           >  2:2603560/1‑101 (MQ=255)                                                                      ccGCGGCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAAcccc                         <  1:4560341/101‑1 (MQ=255)                                                                         cgacATCGAGCGCATCAGGGCGGAGCCGAGGCGGCCGGGGCCGCGCCGGGGGCAGCCGCAGCGTGAACCCGCCGTCCCCGCCCGCCTGCACCAACCCCAcc                      <  1:3319116/98‑1 (MQ=255)                                                                          ggCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCt                     >  2:1518009/1‑101 (MQ=255)                                                                           gCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTc                    >  2:2677362/1‑101 (MQ=255)                                                                           gCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTc                    >  1:1574588/1‑101 (MQ=255)                                                                           gCATCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTc                    >  1:660324/1‑101 (MQ=255)                                                                              tCGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGc                 >  1:3236288/1‑101 (MQ=255)                                                                               cGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCa                >  1:3336864/1‑101 (MQ=255)                                                                               cGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCa                >  2:4111720/1‑101 (MQ=255)                                                                               cGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCa                >  2:5011929/1‑101 (MQ=255)                                                                               cGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCa                >  2:911556/1‑101 (MQ=255)                                                                               cGAGCGCATCAAGGCGCAGCGCATGCGGCCCGGGCGTCCCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCGTGCACCAACCCCACCTCGGcc                >  1:2078266/1‑100 (MQ=255)                                                                                  gcgcATCAAGGCGCAGCGCATGCGGCCGGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTg             <  2:100680/98‑1 (MQ=255)                                                                                  gcgcATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTg             >  2:1029014/4‑101 (MQ=255)                                                                                  gcgcATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTg             >  2:3124845/4‑101 (MQ=255)                                                                                    gcATCAGGGCCCGGCGCGTGCGGCCGGGGCGCCGCCGCGGGCAGCCGCAGCGTGAACCCGCCGCCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTc           <  1:911661/100‑1 (MQ=255)                                                                                    gcATCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTc           >  2:4049855/2‑101 (MQ=255)                                                                                      agaagggCGCGGCGCATGCGCCCGGGGCGCCCCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGa         <  1:2603741/96‑1 (MQ=255)                                                                                      aTCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGa         <  2:911768/101‑1 (MQ=255)                                                                                      aTCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGa         >  2:1819384/1‑101 (MQ=255)                                                                                       tCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCCTTGTCGAc        >  2:3773786/1‑101 (MQ=255)                                                                                       tCAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGAc        >  1:2949578/1‑101 (MQ=255)                                                                                        cAAGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACa       >  2:3294878/1‑101 (MQ=255)                                                                                         aaGGCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACac      >  1:1316655/1‑100 (MQ=255)                                                                                           ggCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAg    >  1:2928231/1‑101 (MQ=255)                                                                                           ggCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAg    <  1:373712/101‑1 (MQ=255)                                                                                           ggCGCAGCGCATGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAg    >  2:755645/1‑101 (MQ=255)                                                                                             cgcagcgcatGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAGgc  >  1:1580355/1‑101 (MQ=255)                                                                                             cgcagcgcatGCGGCCCGGGCGTCGCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAGgc  >  2:2843387/1‑101 (MQ=255)                                                                                                 |                                                                                                 CGGCGGCGGCGGGCGGCGGCGGCGGGGCGACGCCCTCGAAGCCCTGCTCGGCGCGGGCCAGCACCCGGCCCGCGGCATCGAGCCCATCAAGGCGCATCGCATGCGGCCCGGGCGTCTCCGCGGGCAGCCGCAGCGTGAAACCGCCGTCCCCGCCCGCCTGCACCAACCCCACCTCGGCATTGTCGACATAGGC  >  NC_014034/2480945‑2481137 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG