Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,206,635	C→G	A77G (GCC→GGC)	rpoD →	RNA polymerase sigma factor RpoD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,206,635	0	C	G	100.0%	82.3 / NA	25	A77G (GCC→GGC)	rpoD	RNA polymerase sigma factor RpoD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (11/14);  total (11/14)

TGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTA  >  NZ_CP009273/3206557‑3206707                                                                               |                                                                         tGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGccgccg                                                               >  1:664393/1‑90 (MQ=255)       ttCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAgg                                                         <  1:634459/90‑1 (MQ=255)               aTGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTcc                                                 <  2:489800/90‑1 (MQ=255)                tGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCa                                                >  1:641213/1‑90 (MQ=255)                    agaagCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCCGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGt                                            <  1:324248/90‑1 (MQ=255)                     gaagCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTg                                           >  1:87554/1‑90 (MQ=255)                        gCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGaa                                        >  1:296388/1‑90 (MQ=255)                                  ccGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCg                              >  2:226095/1‑90 (MQ=255)                                       gatCTGATGCTGGCTGAAAACCCCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc                         <  2:388257/90‑1 (MQ=255)                                       gatCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc                         <  1:442417/90‑1 (MQ=255)                                       gatCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc                         <  2:159929/90‑1 (MQ=255)                                        atCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCa                        <  2:87554/90‑1 (MQ=255)                                        atCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCa                        >  2:475800/1‑90 (MQ=255)                                             aTGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACt                   <  1:636770/90‑1 (MQ=255)                                                 tggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGAcc               >  1:137873/1‑90 (MQ=255)                                                  ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCa                                                           <  1:472009/45‑1 (MQ=255)                                                  ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCa                                                           >  2:472009/1‑45 (MQ=255)                                                  ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGc                                                      >  1:588261/1‑50 (MQ=255)                                                  ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGc                                                      <  2:588261/50‑1 (MQ=255)                                                  ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGAccc              <  2:664393/90‑1 (MQ=255)                                                     tgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGt           <  1:431183/90‑1 (MQ=255)                                                      gAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTa          <  2:594467/90‑1 (MQ=255)                                                        aaaCACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACg        <  2:367696/90‑1 (MQ=255)                                                             ccGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGt   >  2:232290/1‑90 (MQ=255)                                                              cgcgGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGTACGCATGTa  >  1:208676/1‑90 (MQ=255)                                                                               |                                                                         TGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTA  >  NZ_CP009273/3206557‑3206707

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑