Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,439,101	T→C	K255E (AAG→GAG)	mepA ←	penicillin‑insensitive murein endopeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,439,101	0	T	C	100.0%	85.1 / NA	25	K255E (AAG→GAG)	mepA	penicillin‑insensitive murein endopeptidase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/8);  total (17/8)

TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG  >  NZ_CP009273/2439015‑2439178                                                                                         |                                                                              tAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTct‑‑cctc                                                                            >  1:363273/1‑90 (MQ=255)       ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGc                                                                        >  1:40113/1‑88 (MQ=255)       ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGc                                                                        <  2:40113/88‑1 (MQ=255)       ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCtt                                                                      >  2:448482/1‑90 (MQ=255)                 cGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTccc                                                            <  2:537541/90‑1 (MQ=255)                   tttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCgg                                                          >  1:222582/1‑90 (MQ=255)                   tttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCgg                                                          >  2:560670/1‑90 (MQ=255)                    ttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGGGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGt                                                         >  1:577779/1‑90 (MQ=255)                     tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGtt                                                        >  2:593850/1‑90 (MQ=255)                     tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGtt                                                        >  2:347295/1‑90 (MQ=255)                                aCGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCa                                             >  2:421169/1‑90 (MQ=255)                                   tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGa                                                   >  2:276582/1‑81 (MQ=255)                                   tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGa                                                   <  1:276582/81‑1 (MQ=255)                                   tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAc                                          >  2:452708/1‑90 (MQ=255)                                   tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAc                                          >  1:270538/1‑90 (MQ=255)                                    gCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAcc                                         >  1:165142/1‑90 (MQ=255)                                      tCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAcc                                         >  1:79387/1‑90 (MQ=255)                                                  gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt                           >  1:408205/1‑90 (MQ=255)                                                  gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGGTCAAACCAGCTTTGCAGTTCt                           >  1:54979/1‑90 (MQ=255)                                                     tGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGcc                        >  1:591539/1‑90 (MQ=255)                                                         aGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGc                    <  2:728033/90‑1 (MQ=255)                                                           gAAGGCGGCAACGGAGGCGGTGTCTTCTCCCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGc                    <  2:79387/90‑1 (MQ=255)                                                                cggcAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATc             <  2:165142/90‑1 (MQ=255)                                                                  gcAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGc           <  2:705968/90‑1 (MQ=255)                                                                        gAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATg     <  2:408268/90‑1 (MQ=255)                                                                           gCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCg  >  1:457738/1‑90 (MQ=255)                                                                                         |                                                                              TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG  >  NZ_CP009273/2439015‑2439178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑