Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,747,876	2 bp→GC	100%	intergenic (‑208/+84)	RCAP_rcc02553 ← / ← RCAP_rcc02554	hypothetical protein/NmrA family protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,747,876	0	C→G	100.0%	70.4	27	intergenic (‑208/+85)	RCAP_rcc02553/RCAP_rcc02554	hypothetical protein/NmrA family protein
Reads supporting (aligned to +/- strand):  new base (27/0):  ref base (0/0):  total (27/0)
*	NC_014034	2,747,877	0	T→C	100.0%	135.7	44	intergenic (‑209/+84)	RCAP_rcc02553/RCAP_rcc02554	hypothetical protein/NmrA family protein
Reads supporting (aligned to +/- strand):  new base (44/0):  ref base (0/0):  total (44/0)

GACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCC.GCGGCCGAGAAGCGCCCGCC.GGCCGGCTGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAGCG  >  NC_014034/2747810‑2747971                                                                     ||                                                                                                gACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGCCGGGCCGGGGGGTGGCCGAGGGCCCTTGGGCCCCTCggggt                                                                  >  2:3280255/1‑100 (MQ=17) gACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGt                                                                 >  2:3177167/1‑101 (MQ=17)                     caGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCa                                             >  2:4313916/1‑101 (MQ=17)                                gcccggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGGCACAGGACCTCTGTGAAGCCTGGCCAAGGCg                                  >  1:613325/1‑101 (MQ=17)                                 cccggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGa                                 >  1:4768487/1‑101 (MQ=18)                                  ctgccccggcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGAt                                >  2:3850297/9‑101 (MQ=18)                                   cggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATg                               >  2:2722409/1‑101 (MQ=18)                                   cggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATg                               >  1:6657914/1‑101 (MQ=18)                                   cggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATg                               >  1:4581203/1‑101 (MQ=18)                                    ggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATgg                              >  2:757934/1‑101 (MQ=18)                                    ggcccgGCGGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATgg                              >  2:2062315/1‑101 (MQ=18)                                    gacccggcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGCCTCAGGACCCCTGTGACGCATGGCCAAGGGGATgg                              >  2:2899044/7‑101 (MQ=18)                                     gcccggcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGc                             >  1:5403698/6‑101 (MQ=18)                                        cggcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCtt                          >  2:732402/3‑101 (MQ=21)                                         ggcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTg                         >  1:2804317/2‑101 (MQ=21)                                          gcgGGCGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTgg                        >  1:1332634/1‑101 (MQ=21)                                            gggcGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGGGATGGCCTTGGcc                      >  2:3274935/4‑101 (MQ=21)                                            gggcGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      >  1:33007/4‑101 (MQ=21)                                            gggcGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      >  1:2446238/4‑101 (MQ=21)                                            gggcGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      >  2:1567750/4‑101 (MQ=21)                                              gcGAGAAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCaa                    >  1:2549207/2‑101 (MQ=21)                                                gagaAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAgg                  >  2:2612706/1‑101 (MQ=21)                                                 agaAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGt                 >  1:2570879/1‑101 (MQ=21)                                                 agaAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGt                 >  2:4604249/1‑101 (MQ=21)                                                  gaAGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTc                >  2:2361209/1‑101 (MQ=21)                                                   aaGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCa               >  2:3347017/1‑101 (MQ=21)                                                   aaGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCa               >  2:4400065/1‑101 (MQ=21)                                                   aaGCGCCCGCCGGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCa               >  1:1063759/1‑101 (MQ=21)                                                       gcccgccgGGCCGGGCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTc           >  2:1840958/1‑101 (MQ=21)                                                           gccgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGc       >  2:247228/5‑101 (MQ=255)                                                           gccgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGc       >  2:5495244/5‑101 (MQ=255)                                                            ccgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGcc      >  1:6498711/4‑101 (MQ=255)                                                             cgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCa     >  2:6031354/3‑101 (MQ=255)                                                             cgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCa     >  1:3547618/3‑101 (MQ=255)                                                             cgggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCa     >  2:4073631/3‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGTGGGTCACAGGACCTATGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGccgg    >  2:1258093/2‑99 (MQ=21)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACCGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  2:3620299/2‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGTTCATGCCAg    >  1:5563270/2‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  1:5670138/2‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  1:3957631/2‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  1:6994188/2‑101 (MQ=255)                                                              gggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  2:2637231/2‑101 (MQ=255)                                                               ggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgc   >  1:5761079/1‑101 (MQ=255)                                                               ggccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgc   >  2:5396087/1‑101 (MQ=255)                                                                gccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGAGCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgcg  >  2:6078085/1‑101 (MQ=255)                                                                gccgggCGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgcg  >  1:5264367/1‑101 (MQ=255)                                                                     ||                                                                                                GACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCC.GCGGCCGAGAAGCGCCCGCC.GGCCGGCTGCTGCCCGAGGGCCTTTGGG.CCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAGCG  >  NC_014034/2747810‑2747971 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG