Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	554,427	A→G	intergenic (+217/‑3)	fimA → / → fimC	type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	554,427	0	A	G	100.0%	20.1 / NA	7	intergenic (+217/‑3)	fimA/fimC	type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (2/5);  total (2/5)

AAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGG  >  NZ_CP009273/554360‑554503                                                                    |                                                                             aaGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGtt                                                        <  2:155447/90‑1 (MQ=255)       ccAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGAt                                                  <  2:91263/90‑1 (MQ=255)         aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc                                                >  2:164302/1‑90 (MQ=255)                                       ttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCa                  <  1:87366/90‑1 (MQ=255)                                                 gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc        <  1:213017/90‑1 (MQ=255)                                                               tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCgg  >  1:148573/1‑82 (MQ=255)                                                               tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCgg  <  2:148573/82‑1 (MQ=255)                                                                    |                                                                             AAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGG  >  NZ_CP009273/554360‑554503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑