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%	106.4 / NA	30	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 (13/17);  total (13/17)

TTTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATT  >  NZ_CP009273/115405‑115564                                                                                     |                                                                             tttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATaa                                                                        <  2:107888/90‑1 (MQ=255)   tctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAAc                                                                      <  1:758035/90‑1 (MQ=255)      ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                   >  1:109276/1‑90 (MQ=255)      ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                   >  2:618295/1‑90 (MQ=255)      ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                   >  2:262631/1‑90 (MQ=255)        gCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTgca                                                                 >  2:315035/1‑90 (MQ=255)        gCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTgca                                                                 >  1:598632/1‑90 (MQ=255)        gCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTgca                                                                 >  2:168665/1‑90 (MQ=255)         cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                <  2:598632/90‑1 (MQ=255)            agaTCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTgcatggc                                                             >  1:232395/1‑90 (MQ=255)                     aTTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAg                                                    <  2:510862/90‑1 (MQ=255)                       ttGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtc                                                  <  2:141682/90‑1 (MQ=255)                          cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                               <  1:146042/90‑1 (MQ=255)                           gcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                              <  2:37195/90‑1 (MQ=255)                            cgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCa                                             <  1:815061/90‑1 (MQ=255)                            cgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCa                                             <  2:515487/90‑1 (MQ=255)                            cgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCa                                             >  1:376038/1‑90 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTGAAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgc                                  >  2:52505/1‑90 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGAt                                                                          >  1:652293/1‑49 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGAt                                                                          <  2:652293/49‑1 (MQ=255)                                          gTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGcgcg                               <  1:618295/90‑1 (MQ=255)                                             tGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                            <  2:376038/90‑1 (MQ=255)                                             tGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                            <  1:224606/90‑1 (MQ=255)                                                  cGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                       >  1:894788/1‑90 (MQ=255)                                                            gTG‑AAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGAttttt             <  1:418773/90‑1 (MQ=255)                                                                 aaTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAt         >  2:755182/1‑90 (MQ=255)                                                                       ccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAt   <  2:670209/90‑1 (MQ=255)                                                                        cAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAtt  <  1:319756/90‑1 (MQ=255)                                                                          gTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                              >  1:75930/1‑44 (MQ=255)                                                                          gTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                              <  2:75930/44‑1 (MQ=255)                                                                                     |                                                                             TTTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTG‑AAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATT  >  NZ_CP009273/115405‑115564

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑