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%	76.1 / NA	23	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 (15/8);  total (15/8)

TGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG  >  NZ_CP009273/554354‑554511                                                                          |                                                                                     tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt                                                                      >  1:332876/1‑90 (MQ=255)  gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa                                                                     <  2:773888/90‑1 (MQ=255)  gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa                                                                     <  2:261565/90‑1 (MQ=255)              cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg                                                         <  1:273663/90‑1 (MQ=255)              cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg                                                         <  1:825339/90‑1 (MQ=255)               aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc                                                        >  2:511756/1‑90 (MQ=255)                       cATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATtata                                                >  2:839843/1‑90 (MQ=255)                                     ccTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAt                                  >  1:494413/1‑90 (MQ=255)                                       ttATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAttt                                >  1:390081/1‑90 (MQ=255)                                        tATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTc                               >  2:810134/1‑90 (MQ=255)                                        tATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTc                               >  2:776504/1‑90 (MQ=255)                                        tATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTc                               >  2:528705/1‑90 (MQ=255)                                          tttttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCgg                             >  2:482357/1‑90 (MQ=255)                                            tttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGcc                           <  1:521449/90‑1 (MQ=255)                                            tttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGcc                           <  2:95476/90‑1 (MQ=255)                                                     aGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAt                  <  1:511756/90‑1 (MQ=255)                                                                aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg       >  1:132730/1‑90 (MQ=255)                                                                aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg       >  1:883739/1‑90 (MQ=255)                                                                aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg       >  1:428894/1‑90 (MQ=255)                                                                 ggCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAggg      >  2:566175/1‑90 (MQ=255)                                                                 ggCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAggg      >  2:788433/1‑90 (MQ=255)                                                                    gTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATCTCGGCCAGCGCCCATGCTGCCGGAGGGATc   <  2:621213/90‑1 (MQ=255)                                                                     tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg  >  2:51202/1‑90 (MQ=255)                                                                          |                                                                                     TGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG  >  NZ_CP009273/554354‑554511

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑