Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,848,051	T→G	F257C (TTT→TGT)	emrD →	multidrug efflux MFS transporter EmrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,848,051	0	T	G	100.0%	64.3 / NA	21	F257C (TTT→TGT)	emrD	multidrug efflux MFS transporter EmrD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (15/6);  total (15/6)

GATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGG  >  NZ_CP009273/3847980‑3848135                                                                        |                                                                                     gATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGc                                                                    >  1:39017/1‑90 (MQ=255)      gcgcGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGAc                                                               >  2:505759/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:105470/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:558696/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:469359/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:417654/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:301088/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:268105/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:231277/1‑90 (MQ=255)                     tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  1:184615/1‑90 (MQ=255)                         cAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTtctc                                            <  1:204067/90‑1 (MQ=255)                           gTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCa                                          >  1:535491/1‑90 (MQ=255)                                  ggTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCgg                                                                 <  1:541982/60‑1 (MQ=255)                                  ggTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCgg                                                                 >  2:541982/1‑60 (MQ=255)                                     cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                >  2:395676/1‑74 (MQ=255)                                     cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                <  1:395676/74‑1 (MQ=255)                                            ttGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCg                         >  1:106599/1‑90 (MQ=255)                                            ttGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCg                         >  2:109694/1‑90 (MQ=255)                                                       gCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATctgctg              <  1:558696/90‑1 (MQ=255)                                                         cGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGctgcc            <  1:505759/90‑1 (MQ=255)                                                                   aGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGctggctgg  <  1:301088/90‑1 (MQ=255)                                                                        |                                                                                     GATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGG  >  NZ_CP009273/3847980‑3848135

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑