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%	94.2 / NA	29	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 (15/14);  total (15/14)

TTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGA  >  NZ_CP009273/115406‑115566                                                                                   |                                                                               ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaa                                                                          <  2:414711/89‑1 (MQ=255) ttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaa                                                                          >  1:414711/1‑89 (MQ=255)       gCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgca                                                                   >  2:333745/1‑90 (MQ=255)        cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                  <  2:432682/90‑1 (MQ=255)        cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTgcat                                                                  <  2:131161/90‑1 (MQ=255)            gaTCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAAc                                                                        >  2:479627/1‑80 (MQ=255)            gaTCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAAc                                                                        <  1:479627/80‑1 (MQ=255)                     tttGCGCGTCTCCGCTCCCTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGt                                                     <  1:443706/90‑1 (MQ=255)                      ttGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtc                                                    <  1:416129/90‑1 (MQ=255)                         cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                 <  1:400331/90‑1 (MQ=255)                          gcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                <  2:293273/90‑1 (MQ=255)                           cgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCa                                               <  2:63191/90‑1 (MQ=255)                                  gCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                <  1:138604/82‑1 (MQ=255)                                  gCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                >  2:138604/1‑82 (MQ=255)                                       cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                   >  2:141378/1‑90 (MQ=255)                                            tGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                              <  1:90640/90‑1 (MQ=255)                                                 cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                         >  1:440423/1‑90 (MQ=255)                                                 cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                         >  2:223059/1‑90 (MQ=255)                                                 cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                         >  2:497310/1‑90 (MQ=255)                                                   ccGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCTGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCaa                       <  1:285508/90‑1 (MQ=255)                                                                aTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCAGGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAtt          <  1:322025/90‑1 (MQ=255)                                                                   gTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTggg       >  2:445696/1‑90 (MQ=255)                                                                   gTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTggg       >  1:108395/1‑90 (MQ=255)                                                                    tCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGa      >  1:280861/1‑90 (MQ=255)                                                                     ccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGAt                   >  1:331963/1‑76 (MQ=255)                                                                     ccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGAt                   <  2:331963/76‑1 (MQ=255)                                                                     ccAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAt     >  1:18504/1‑90 (MQ=255)                                                                        gTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCCCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGa  >  1:470570/1‑90 (MQ=255)                                                                        gTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGGCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGa  >  2:27196/1‑90 (MQ=255)                                                                                   |                                                                               TTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGA  >  NZ_CP009273/115406‑115566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑