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%	68.6 / NA	22	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 (7/15);  total (7/15)

TCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGA  >  NZ_CP009273/115407‑115572                                                                                  |                                                                                     tctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTTTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAAc                                                                              <  1:594297/90‑1 (MQ=255)    ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                           >  1:239449/1‑90 (MQ=255)      gCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgca                                                                         >  1:14335/1‑90 (MQ=255)       cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                        <  1:1291/90‑1 (MQ=255)       cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                        <  1:51508/90‑1 (MQ=255)                   aTTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAg                                                            <  2:97793/90‑1 (MQ=255)                    tttGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGt                                                           <  1:445239/90‑1 (MQ=255)                    tttGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGt                                                           <  2:250043/90‑1 (MQ=255)                     ttGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtc                                                          <  1:246298/90‑1 (MQ=255)                        cgcgTCTCCGCTCGCTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                       <  2:351351/90‑1 (MQ=255)                        cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                       <  1:637771/90‑1 (MQ=255)                                   tCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAggg                                            <  2:290836/90‑1 (MQ=255)                                      cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                         >  1:59302/1‑90 (MQ=255)                                           tGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                                    <  2:14335/90‑1 (MQ=255)                                                          gTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGAttttt                     <  1:77503/90‑1 (MQ=255)                                                            gAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGc                                                                 <  1:6394/44‑1 (MQ=255)                                                            gAAATAGTCCAGTATGTTCCTTCCGATAAACGAGCATGGCATGc                                                                 >  2:6394/1‑44 (MQ=255)                                                              aaTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAt                 >  2:234615/1‑90 (MQ=255)                                                               aTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAtt                <  1:487470/90‑1 (MQ=255)                                                                    ccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAt           >  2:284032/1‑90 (MQ=255)                                                                         aTGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGc      >  1:402626/1‑90 (MQ=255)                                                                            ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg   >  2:180132/1‑90 (MQ=255)                                                                            ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg   >  1:654689/1‑90 (MQ=255)                                                                            ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg   >  1:508602/1‑90 (MQ=255)                                                                             tCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGa  <  2:59302/90‑1 (MQ=255)                                                                                  |                                                                                     TCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGA  >  NZ_CP009273/115407‑115572

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑