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%	74.4 / 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)

TTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATCCC  >  NZ_CP009273/115557‑115714                                                                        |                                                                                       ttGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCCGGGCCTgattgatt                                                                      >  2:97447/1‑90 (MQ=255)   gggATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGc                                                                    <  1:57941/90‑1 (MQ=255)    ggATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCt                                                                   <  1:592889/90‑1 (MQ=255)     gATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTa                                                                  >  1:104568/1‑90 (MQ=255)       ttGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATc                                                                <  2:104568/90‑1 (MQ=255)        tGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATcc                                                               >  1:355848/1‑90 (MQ=255)             ttGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGata                                                          >  1:62188/1‑90 (MQ=255)               gAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATc                                                        >  1:532668/1‑90 (MQ=255)                   gCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTa                                                    <  2:62188/90‑1 (MQ=255)                            cGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGa                                           >  1:494908/1‑90 (MQ=255)                                  cGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGcc                                     <  1:234615/90‑1 (MQ=255)                                  cGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGcc                                     <  2:532668/90‑1 (MQ=255)                                    tataCCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCAt                                   <  1:396194/90‑1 (MQ=255)                                      taCCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTTATTTCTATCCGGGTATCGCTAAAAACATGACGGGCCATtg                                 >  2:281536/1‑90 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGGACTGGTTGATTGCTATCCGGGTATCGCTAAAAACATGACGGGCCATtgtggt                             >  2:438421/1‑88 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACt                                                                              >  1:213298/1‑41 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACt                                                                              <  2:213298/41‑1 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                             >  1:15502/1‑90 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                             >  1:496805/1‑90 (MQ=255)                                          gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                             >  1:212842/1‑90 (MQ=255)                                               gcAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTgc                        >  1:897/1‑90 (MQ=255)                                                            cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTa                                                    <  2:427922/49‑1 (MQ=255)                                                            cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTa                                                    >  1:427922/1‑49 (MQ=255)                                                            cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAAAATGACGGGCCATTTTGATATTGCGCCGGATCGGgaa           >  2:625572/1‑90 (MQ=255)                                                              tGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAAc         >  1:296152/1‑90 (MQ=255)                                                                     gTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATccc  <  2:64993/90‑1 (MQ=255)                                                                     gTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATccc  <  1:17208/90‑1 (MQ=255)                                                                        |                                                                                       TTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCGATCCC  >  NZ_CP009273/115557‑115714

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑