Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	49,884	C→T	P21L (CCG→CTG)	folA →	type 3 dihydrofolate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	49,884	0	C	T	83.3%	43.7 / 1.1	24	P21L (CCG→CTG)	folA	type 3 dihydrofolate reductase
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base T (7/13);  total (7/17)
Fisher's exact test for biased strand distribution p-value = 2.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-01

ATTTTTTTTATCGGGAAATCTCAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAT  >  NZ_CP009273/49800‑49957                                                                                     |                                                                          aTTTTTTTTATCGGGAAATCTCAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGa                                                                      <  1:239721/90‑1 (MQ=255) aTTTTTTTTATCGGGAAATCTCAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGa                                                                      <  2:148793/90‑1 (MQ=255)           tCGGGAAATCTCAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCGTGCTGTGGAACctgcctgc                                                            <  1:101792/90‑1 (MQ=255)                     tcAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGcc                                                  <  2:112925/90‑1 (MQ=255)                            taattCTGATTGCGGCGTGACCGGTAAAACGGATTAACGTCATGGAAAACGCCCTGTTGTGGACCCTGCCTGCCGATCTCGCCTGGTTTa                                           <  2:378892/86‑1 (MQ=255)                             cAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTaa                                          >  1:277220/1‑90 (MQ=255)                                   gATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCaa                                    <  1:151815/90‑1 (MQ=255)                                   gATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCaa                                    <  1:548321/90‑1 (MQ=255)                                   gATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCaa                                    <  1:267814/90‑1 (MQ=255)                                    aTTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAac                                   <  2:574406/90‑1 (MQ=255)                                        cggcgTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCt                               <  1:345248/90‑1 (MQ=255)                                         ggcgTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCtt                              >  1:541235/1‑90 (MQ=255)                                         ggcgTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCtt                              >  2:20845/1‑90 (MQ=255)                                         ggcgTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCtt                              >  2:247845/1‑90 (MQ=255)                                             ttAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTtaaat                          >  1:49821/1‑90 (MQ=255)                                                  ggTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAAcc                     <  2:320425/90‑1 (MQ=255)                                                        tCGCGTTATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGAt               >  1:86103/1‑90 (MQ=255)                                                             ttATCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATgg          <  1:261405/90‑1 (MQ=255)                                                               aTCGGCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGgc        <  2:418875/90‑1 (MQ=255)                                                                  ggCATGGAAAACGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGgccgc     <  1:507567/90‑1 (MQ=255)                                                                     aTGGAAAACGCCATCCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAt  <  1:430115/90‑1 (MQ=255)                                                                     aTGAAAACCCCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAt  <  2:49821/90‑1 (MQ=255)                                                                             cGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAt  <  2:582850/82‑1 (MQ=255)                                                                             cGCCATGCTGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAt  >  1:582850/1‑82 (MQ=255)                                                                                     |                                                                          ATTTTTTTTATCGGGAAATCTCAATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCAT  >  NZ_CP009273/49800‑49957

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑