Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	115,628	A→C	T137P (ACG→CCG)	ampD →	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	115,628	0	A	C	100.0%	72.7 / NA	27	T137P (ACG→CCG)	ampD	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (16/11);  total (16/11)

GGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATCCC  >  NZ_CP009273/115559‑115714                                                                      |                                                                                       gggATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGc                                                                    <  2:94067/90‑1 (MQ=255)                   aCCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTTATTGCTATCCGGGTATCGCTaaa                                                  >  2:605012/1‑90 (MQ=255)                    ccGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTaaaa                                                 >  2:318240/1‑90 (MQ=255)                             tGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACgg                                        <  2:528356/90‑1 (MQ=255)                                cGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGcc                                     <  2:556000/90‑1 (MQ=255)                                 gTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCCCTCATTTGTTTGTATCCAGATATCACTCAAAAAAAGACGGGcct                                    >  1:217029/1‑89 (MQ=255)                                  tataCCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCAt                                   <  1:337164/90‑1 (MQ=255)                                  tataCCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCAt                                   <  2:44823/90‑1 (MQ=255)                                  tataCCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCAt                                   <  2:34391/90‑1 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGGACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGGCATTTTGat                             >  2:488349/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGGACTGATTGATTGCTATCCGGATATCGCTAAAAAAATGACGGGGCCTTGTGat                             >  1:399729/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTTATTGCTATCCGGGTATCGCTAAAAACATGACGGGGCCTTGTGat                             >  1:512763/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                             >  1:94341/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACCGGTTGATTGCTATCCGGAAATCGCCAAAAAAAAGACGGGCCCTTGTGat                             >  1:346967/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACCGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                             >  1:459332/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGTTCCCCGGGCCCTGATTGATTGCTATCCCGGTATCGCTAAAAACAAGACGGGCCATTGTGat                             >  2:337164/1‑90 (MQ=255)                                        gATGCGCAGTATCAACAGCTTGCGGCGGATCCGGGGGCACTGATTGATTTCTATCCGGGGATCGCTAAAAACATGACGGGCCGTtgtggt                             >  2:392562/1‑88 (MQ=255)                                                gTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGcc                                     <  1:139098/74‑1 (MQ=255)                                                gTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGcc                                     >  2:139098/1‑74 (MQ=255)                                                  aTCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCgg                   <  2:367240/90‑1 (MQ=255)                                                     aaCAGCTTGCGGCGGTTCCGCGGGGACTGATTGTTTGCTATCCGGGTATCGCTAAAAAAAAGACGGGCCCTTTTGATATTTCGCCGGGTc                >  1:585757/1‑90 (MQ=255)                                                          cTTGCGGCGGTTCCGCGGGCACTGATTGATTTCTATCCGGGTATTGCTAAAAAAATGACGGGGCATTTTGATATTTCGCCGGGTCGGaaa           >  1:352784/1‑90 (MQ=255)                                                          cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGAc                                          <  2:335131/59‑1 (MQ=255)                                                          cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGAc                                          >  1:335131/1‑59 (MQ=255)                                                          cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAAAATGACGGGCCCTTGTGATATTTCGCCGGATCGGaaa           >  1:475930/1‑90 (MQ=255)                                                              cggcggTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCg       <  2:515505/90‑1 (MQ=255)                                                                   gTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATccc  <  2:67628/90‑1 (MQ=255)                                                                      |                                                                                       GGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATCCC  >  NZ_CP009273/115559‑115714

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑