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%	119.6 / NA	35	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 (13/22);  total (13/22)

TTTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGAAG  >  NZ_CP009273/115405‑115574                                                                                    |                                                                                       tttctttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATaa                                                                                  <  2:645997/90‑1 (MQ=255)      ttGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTg                                                                             >  1:680723/1‑90 (MQ=255)         cTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCCTCCGATAAACGTgcat                                                                          <  1:691510/90‑1 (MQ=255)                   ccATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCggg                                                                <  1:1040045/90‑1 (MQ=255)                     aTTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAg                                                              <  1:732033/90‑1 (MQ=255)                          cgcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctct                                                         <  1:322576/90‑1 (MQ=255)                           gcgTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                        <  1:1126090/90‑1 (MQ=255)                              tctcCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGt                                                     <  1:690074/90‑1 (MQ=255)                                 ccGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATc                                                  <  2:1018419/90‑1 (MQ=255)                                   gCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAg                                                <  1:396666/90‑1 (MQ=255)                                   gCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAg                                                <  2:18474/90‑1 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                           >  2:990572/1‑90 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                           >  2:260770/1‑90 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                           >  1:721258/1‑90 (MQ=255)                                        cTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcg                                           >  1:37995/1‑90 (MQ=255)                                         tGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGgcgc                                          >  2:583036/1‑90 (MQ=255)                                          gTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGcgcg                                         >  2:693214/1‑90 (MQ=255)                                             tGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAAc                                      <  1:466914/90‑1 (MQ=255)                                               aTTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGc                                    <  2:619840/90‑1 (MQ=255)                                               aTTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGc                                    <  2:336872/90‑1 (MQ=255)                                                  cGCCGTGATGGTGAAATAGTCCAGTCTGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                        <  1:561445/67‑1 (MQ=255)                                                  cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGtctctc                                                        >  2:561445/1‑67 (MQ=255)                                                  cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                                 >  1:981941/1‑90 (MQ=255)                                                  cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                                 >  1:814286/1‑90 (MQ=255)                                                  cGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGc                                 >  2:427760/1‑90 (MQ=255)                                                      gTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATg                             <  1:427760/90‑1 (MQ=255)                                                      gTGATGGTGAAATAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATg                             <  1:583036/90‑1 (MQ=255)                                                                aaTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAt                   <  2:242810/90‑1 (MQ=255)                                                                aaTAGTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTAt                   <  2:578646/90‑1 (MQ=255)                                                                    gTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTggg               >  2:648782/1‑90 (MQ=255)                                                                    gTCCAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTggg               >  2:270353/1‑90 (MQ=255)                                                                       cAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAtt            <  2:608005/90‑1 (MQ=255)                                                                       cAGTATGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGAtt            <  1:410396/90‑1 (MQ=255)                                                                           aTGTTCCTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGc        <  2:130662/90‑1 (MQ=255)                                                                              ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg     >  2:251550/1‑90 (MQ=255)                                                                              ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg     >  2:113854/1‑90 (MQ=255)                                                                              ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg     >  2:1034530/1‑90 (MQ=255)                                                                              ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg     >  2:811396/1‑90 (MQ=255)                                                                              ttccttccGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTg     >  1:726268/1‑90 (MQ=255)                                                                                 cTTCCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGAAg  <  1:446621/90‑1 (MQ=255)                                                                                    |                                                                                       TTTCTTTGCTGAGATCGCCCATTTGCGCGTCTCCGCTCACTGTTTGATTCGCCGTGATGGTGAAATAGTCCAGTATGTTCCTTTCGATAAACGTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGCGAACGCTGCAATGATTTTTCTATTGGGATTGAGCTTGAAG  >  NZ_CP009273/115405‑115574

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: ‑