Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,656,518	T→C	D915D (GAT→GAC)	mdtF →	multidrug efflux pump RND permease MdtF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,656,518	0	T	C	100.0%	64.4 / NA	22	D915D (GAT→GAC)	mdtF	multidrug efflux pump RND permease MdtF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/5);  total (17/5)

CGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCT  >  NZ_CP009273/3656434‑3656598                                                                                     |                                                                                 cgcACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTgcg                                                                             <  2:315161/90‑1 (MQ=255)               gccggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCt                                                                        >  2:450633/4‑81 (MQ=255)               gccggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCt                                                                        <  1:450633/78‑1 (MQ=255)               gCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATg                                                               >  1:25472/1‑90 (MQ=255)               gCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATg                                                               >  1:78408/1‑90 (MQ=255)                 tGGTCAATTCCGTTCTCGGTGGTGTTGGTTGTTCCGTTAGGCGTCGTAGGCGCATTACTGGCCCCCGACCTGCGCGGCTTAAGAAGTGAc                                                             >  2:421853/1‑90 (MQ=255)                 tGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc                                                             >  1:301140/1‑90 (MQ=255)                 tGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc                                                             >  2:316719/1‑90 (MQ=255)                  ggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc                                                             <  1:256863/89‑1 (MQ=255)                  ggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc                                                             >  2:256863/1‑89 (MQ=255)                     cAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCt                                                         <  2:78408/90‑1 (MQ=255)                            gTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCa                                                  >  2:120673/1‑90 (MQ=255)                            gTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCa                                                  >  2:113910/1‑90 (MQ=255)                               ctcGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggt                                               <  2:60805/90‑1 (MQ=255)                                 cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg                                             >  2:123949/1‑90 (MQ=255)                                 cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg                                             >  1:349693/1‑90 (MQ=255)                                 cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg                                             >  2:318518/1‑90 (MQ=255)                                 cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg                                             >  1:253933/1‑90 (MQ=255)                                                    gTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCgg                          >  1:270842/1‑90 (MQ=255)                                                           gtcgtTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTcc                   >  2:173591/1‑90 (MQ=255)                                                                tGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCaa              >  1:336628/1‑90 (MQ=255)                                                                            ggCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCt  >  2:162562/1‑90 (MQ=255)                                                                                     |                                                                                 CGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCT  >  NZ_CP009273/3656434‑3656598

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑