Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,423,602	T→C	R99R (CGT→CGC)	stfR →	prophage tail fiber N‑terminal domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,423,602	0	T	C	100.0%	27.0 / NA	10	R99R (CGT→CGC)	stfR	prophage tail fiber N‑terminal domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/6);  total (4/6)

GGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCAC  >  NZ_CP009273/1423522‑1423669                                                                                 |                                                                    gggACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCa                                                            >  1:208190/1‑90 (MQ=255)       aTTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTgcgc                                                      <  2:251791/90‑1 (MQ=255)             gtgtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGtttt                                                >  2:162873/1‑90 (MQ=255)               gtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGa                                              >  1:403146/1‑90 (MQ=255)                   gAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTg                                          <  1:488067/90‑1 (MQ=255)                     aGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGAt                                        <  2:256985/90‑1 (MQ=255)                                                         tGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGc    >  2:40326/1‑90 (MQ=255)                                                           ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac  <  1:376758/90‑1 (MQ=255)                                                           ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac  <  1:98055/90‑1 (MQ=255)                                                           ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac  <  2:403146/90‑1 (MQ=255)                                                                                 |                                                                    GGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCAC  >  NZ_CP009273/1423522‑1423669

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑