Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	354,025	T→C	E126G (GAA→GGA)	cynR ←	transcriptional regulator CynR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	354,025	0	T	C	100.0%	74.6 / NA	21	E126G (GAA→GGA)	cynR	transcriptional regulator CynR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/11);  total (10/11)

CCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGG  >  NZ_CP009273/353942‑354106                                                                                    |                                                                                  ccGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTa                                                                             >  2:210358/1‑90 (MQ=255)      gAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTgg                                                                        <  1:159059/90‑1 (MQ=255)       aaTGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGa                                                                       >  1:166813/1‑90 (MQ=255)        aTGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAg                                                                      <  1:545216/90‑1 (MQ=255)            acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg                                                                  <  1:425970/90‑1 (MQ=255)            acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg                                                                  <  2:179359/90‑1 (MQ=255)              aGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGAt                                                                <  1:56403/90‑1 (MQ=255)                       ggCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATa                                                       <  2:166813/90‑1 (MQ=255)                         cAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgc                                                     >  2:274125/1‑90 (MQ=255)                            tCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgcgcg                                                  <  2:445462/90‑1 (MQ=255)                                     ccAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAAt                                         >  2:120359/1‑90 (MQ=255)                                      cAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATc                                        >  1:422412/1‑90 (MQ=255)                                      cAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATc                                        <  1:53951/90‑1 (MQ=255)                                          tcgtcgCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGcc                                    <  1:313624/90‑1 (MQ=255)                                            gtcgCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCAt                                  >  1:172673/1‑90 (MQ=255)                                                   cAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgggg                           <  1:210358/90‑1 (MQ=255)                                                                cGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGc              >  2:435494/1‑90 (MQ=255)                                                                       ctcCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTaaa       >  1:365294/1‑90 (MQ=255)                                                                           tGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTg   <  2:273296/90‑1 (MQ=255)                                                                            gCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTgg  >  1:365666/1‑90 (MQ=255)                                                                            gCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCACGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTgg  >  2:465058/1‑90 (MQ=255)                                                                                    |                                                                                  CCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGG  >  NZ_CP009273/353942‑354106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑