Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,554,121	A→C	N169T (AAC→ACC)	BW25113_RS12740 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,554,121	0	A	C	100.0%	54.7 / NA	17	N169T (AAC→ACC)	BW25113_RS12740	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (9/8);  total (9/8)

CACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA  >  NZ_CP009273/2554058‑2554203                                                                |                                                                                   cacaGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTc                                                          >  1:287240/1‑90 (MQ=255)                        ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:310638/1‑90 (MQ=255)                        ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:147822/1‑90 (MQ=255)                        ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:167100/1‑90 (MQ=255)                             gggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCg                              >  1:136293/1‑90 (MQ=255)                             gggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCg                              <  1:3754/90‑1 (MQ=255)                               gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  1:237221/1‑90 (MQ=255)                                  cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg                         <  2:61908/90‑1 (MQ=255)                                  cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg                         <  1:277916/90‑1 (MQ=255)                                   aaTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc                                                 >  1:275227/1‑65 (MQ=255)                                   aaTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc                                                 <  2:275227/65‑1 (MQ=255)                                   aaTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGa                        >  2:79703/1‑90 (MQ=255)                                    aTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGaa                       <  1:210418/90‑1 (MQ=255)                                    aTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGaa                       <  1:10918/90‑1 (MQ=255)                                       gACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGc                    <  2:342089/90‑1 (MQ=255)                                         cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta                  <  1:75419/90‑1 (MQ=255)                                                         tCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCa  >  1:99885/1‑90 (MQ=255)                                                                |                                                                                   CACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA  >  NZ_CP009273/2554058‑2554203

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: ‑