Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,650,516	T→C	G54G (GGT→GGC)	hdeD →	acid‑resistance protein HdeD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,650,516	0	T	C	100.0%	19.5 / NA	8	G54G (GGT→GGC)	hdeD	acid‑resistance protein HdeD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/5);  total (3/5)

GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATC  >  NZ_CP009273/3650429‑3650596                                                                                        |                                                                                 gTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                <  2:200205/90‑1 (MQ=255)           gTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                >  1:105691/1‑80 (MQ=255)           gTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGgcgc                                                                                <  2:105691/80‑1 (MQ=255)                  tgTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATc                                                                      <  1:108315/83‑1 (MQ=255)                  tgTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATc                                                                      >  2:108315/1‑83 (MQ=255)                        tcgtcgGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTg                                                         >  1:115367/1‑90 (MQ=255)                            cgGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCt                                                     <  2:291204/90‑1 (MQ=255)                                               ttCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGc                                  >  1:314661/1‑90 (MQ=255)                                                                 gATATTTTAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTc                <  2:209502/90‑1 (MQ=255)                                                                        tAAGCACAGTAGTGGGCGCATTATTAATCTGCTCGGGTATTGGGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCgg         <  2:314661/90‑1 (MQ=255)                                                                               agtagtGGGCGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATc  <  2:309844/90‑1 (MQ=255)                                                                                        |                                                                                 GTTTATTGCCGTGCTGCTGTTTATCGTCGGGTTGCTGTGTATCAGTTTCCCGTTCGTCTCTGGCGATATTTTAAGCACAGTAGTGGGTGCATTATTAATCTGCTCGGGTATTGCGCTTATTGTCGGGTTATTCAGCAACCGCAGTCATAATTTCTGGCCGGTATTATC  >  NZ_CP009273/3650429‑3650596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑