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%	99.9 / NA	38	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 (26/12);  total (26/12)

TGATTTTTCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCG  >  NZ_CP009273/115546‑115709                                                                                   |                                                                                  tGATTTTTCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGc                                                                            <  1:74043/90‑1 (MQ=255) tGATTTTTCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGc                                                                            <  1:315879/90‑1 (MQ=255)   aTTTTTCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCAc                                                                          <  2:334457/90‑1 (MQ=255)     ttttCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACtg                                                                        >  1:291587/1‑90 (MQ=255)       ttCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGGCCtgat                                                                      >  1:731885/1‑90 (MQ=255)                     aGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCCCGGGGACTGCTTGGTTTCTATCCgg                                                        >  1:576532/1‑90 (MQ=255)                         tGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGatat                                                    >  1:275562/1‑90 (MQ=255)                                       cGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGa                                      >  2:289124/1‑90 (MQ=255)                                          tGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACgg                                   <  1:186646/90‑1 (MQ=255)                                            gCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGc                                 <  2:275562/90‑1 (MQ=255)                                              gTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACCGGTTTATTGCTATCCGGGTATCGCTAAAAACATGACGGGccc                               >  1:684457/1‑89 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCgg                                                                              >  1:297416/1‑36 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCgg                                                                              <  2:297416/36‑1 (MQ=39)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTTCTATCCGGAAATCGCTAAAAAAATGAAGGGCCAAtgtggt                        >  2:618337/1‑88 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGGTATCGCTAAAAACATGACGGGGCATTGTGat                        >  1:445425/1‑90 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGc                                 <  2:605385/81‑1 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGc                                 >  1:605385/1‑81 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                        >  2:514992/1‑90 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGat                        >  2:218346/1‑90 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAAAATGACGGGCCATTGTGat                        >  1:380352/1‑90 (MQ=255)                                                     gATGCGCAGTATCAACAGCTTGCGGCGGTTCCCCGGGCACTGATTGATTGCTATCCGGATATTGCTAAAAACATGACGGGCCCTtgtggt                        >  2:837539/1‑88 (MQ=255)                                                        gcgcAGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATAtt                     >  2:673438/1‑90 (MQ=255)                                                          gcAGTATCAACAGCTTGCGGCGGTTCCGCGGGGACTGATTTATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGTTATTgc                   >  1:144166/1‑90 (MQ=255)                                                            aGTATCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTgcgc                 <  2:684457/90‑1 (MQ=255)                                                               aTCAACAGCTTGCGGCGGTTCCGCGGGGACTGATTGATTGCTATCCGGGTATCGCTAAAAAAAAGGCGGGCCCTTGTGATATTTCGcccg              >  1:1002438/1‑88 (MQ=255)                                                               aTCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCgg              <  1:733929/90‑1 (MQ=255)                                                               aTCAACAGCTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCgg              <  2:576532/90‑1 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCCCTGATTTATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGGTCGGgaa      >  1:217326/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTTATTTATTGCTATCCGGATATCGCTAAAAACATGACGGGGCCTTGTGATATTTCGCCGGATCGGgaa      >  1:578907/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAAc                                          <  1:389008/54‑1 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAAc                                          >  2:389008/1‑54 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTTCGCCCGGTCGGaaa      >  1:27692/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGaaa      >  2:185110/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGaaa      >  2:134897/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGaaa      >  1:16696/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACCGGCCATTTGGATATTGCGCCGGATCGGaaa      >  2:697345/1‑90 (MQ=255)                                                                       cTTGCGGCGGTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACAAGACGGGGCCTTGGGATATTTCGCCGGGGCGGaaa      >  1:769707/1‑90 (MQ=255)                                                                           cggcggTTCCGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCg  <  1:246690/90‑1 (MQ=255)                                                                                   |                                                                                  TGATTTTTCTATTGGGATTGAGCTTGAAGGCACCGATACGCTGGCGTATACCGATGCGCAGTATCAACAGCTTGCGGCGGTTACGCGGGCACTGATTGATTGCTATCCGGATATCGCTAAAAACATGACGGGCCATTGTGATATTGCGCCGGATCGGAAAACCG  >  NZ_CP009273/115546‑115709

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑