Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,520,900	T→C	I358T (ATC→ACC)	igaA →	intracellular growth attenuator protein IgaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,520,900	0	T	C	100.0%	80.8 / NA	23	I358T (ATC→ACC)	igaA	intracellular growth attenuator protein IgaA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/14);  total (9/14)

AAAACTTTCCGTTACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGATCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAGCCACCAGC  >  NZ_CP009273/3520816‑3520970                                                                                     |                                                                       aaaaCTTTCCGTTACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGc                                                                   <  1:30112/90‑1 (MQ=255)  aaaCTTTCCGTTACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGGGCTGTTTATGCTGTTATTCTGGACCCCGCt                                                                  >  1:378813/1‑90 (MQ=255)       ttCCGTTACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGata                                                             >  2:115612/1‑90 (MQ=255)             tACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGc                                                       <  1:115612/90‑1 (MQ=255)                      ggCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCa                                              >  2:65456/1‑90 (MQ=255)                      ggCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCa                                              >  2:347947/1‑90 (MQ=255)                      ggCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCa                                              >  2:16537/1‑90 (MQ=255)                      ggCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCa                                              >  1:456762/1‑90 (MQ=255)                      ggCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCa                                              >  1:48049/1‑90 (MQ=255)                         tGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCActc                                           <  1:423157/90‑1 (MQ=255)                               gTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCAt                                     <  1:65225/90‑1 (MQ=255)                               gTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCAt                                     <  2:48049/90‑1 (MQ=255)                               gTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCAt                                     <  1:26176/90‑1 (MQ=255)                                         cGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAgg                           >  1:134289/1‑90 (MQ=255)                                         cGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAgg                           <  1:117298/90‑1 (MQ=255)                                              cGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGgcgcgc                      <  2:108573/90‑1 (MQ=255)                                                ggCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAg                    <  1:28869/90‑1 (MQ=255)                                                ggCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAg                    <  2:307530/90‑1 (MQ=255)                                                         ctgGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGaa           <  2:498620/90‑1 (MQ=255)                                                          tgGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAg          <  1:347947/90‑1 (MQ=255)                                                          tgGTGCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAg          >  2:383856/1‑90 (MQ=255)                                                              gCTGTTTATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAGccac      <  2:456762/90‑1 (MQ=255)                                                                  tttATGCTGTTATTCTGGACCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAGCCACCAGc  <  2:378813/90‑1 (MQ=255)                                                                                     |                                                                       AAAACTTTCCGTTACAGCACTGGCTGCGCAGTACGATTATCGCTGCGGGCTCGCTGCTGGTGCTGTTTATGCTGTTATTCTGGATCCCGCTGGATATGCCGCTGAAATTCACTCTCTCATGGATGAAAGGCGCGCAGACCATTGAAGCCACCAGC  >  NZ_CP009273/3520816‑3520970

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑