Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	115,488	T→C	F90S (TTC→TCC)	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	115,488	0	T	C	100.0%	91.2 / NA	27	F90S (TTC→TCC)	ampD	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/16);  total (11/16)

TTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTG  >  NZ_CP009273/115406‑115571                                                                                   |                                                                                    ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaaa                                                                              >  2:279146/1‑90 (MQ=255) ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaaa                                                                              <  1:265846/90‑1 (MQ=255) ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaaa                                                                              >  2:166357/1‑90 (MQ=255) ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaaa                                                                              >  1:45625/1‑90 (MQ=255)     ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                          >  1:138020/1‑90 (MQ=255)     ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                          >  1:437334/1‑90 (MQ=255)        cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                       <  1:20942/90‑1 (MQ=255)        cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                       <  1:407581/90‑1 (MQ=255)        cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                       <  2:268913/90‑1 (MQ=255)               cGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGc                                                                <  1:182780/90‑1 (MQ=255)                    aTTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAg                                                           >  2:28818/1‑90 (MQ=255)                         cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                      <  1:310226/90‑1 (MQ=255)                         cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                      <  1:123644/90‑1 (MQ=255)                          gcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                     <  1:50859/90‑1 (MQ=255)                          gcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                     <  2:312219/90‑1 (MQ=255)                           cgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCa                                                    <  2:82066/90‑1 (MQ=255)                                  gCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAg                                             <  2:277074/90‑1 (MQ=255)                                            tGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                                   <  2:407089/90‑1 (MQ=255)                                               ttCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCt                                <  2:298615/90‑1 (MQ=255)                                                 cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                              >  1:412161/1‑90 (MQ=255)                                                 cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                              >  2:466568/1‑90 (MQ=255)                                                           gTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGAttttt                    <  1:214371/90‑1 (MQ=255)                                                                aTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAtt               <  2:143130/90‑1 (MQ=255)                                                                 tAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTg              >  1:195990/1‑90 (MQ=255)                                                                   gaccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTggg            >  1:232951/3‑90 (MQ=255)                                                                    tCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGa           >  2:325033/1‑90 (MQ=255)                                                                       aGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTg        <  2:232951/90‑1 (MQ=255)                                                                             ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg  >  1:432539/1‑90 (MQ=255)                                                                             ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg  >  2:266364/1‑90 (MQ=255)                                                                                   |                                                                                    TTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTG  >  NZ_CP009273/115406‑115571

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑