Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,613,753	(A)6→5	coding (377/435 nt)	marR →	multiple antibiotic resistance transcriptional regulator MarR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,613,748	0	A	.	95.8%	90.8 / ‑1.2	24	coding (372/435 nt)	marR	multiple antibiotic resistance transcriptional regulator MarR
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (15/8);  total (15/9)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01

ACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG  >  NZ_CP009273/1613664‑1613833                                                                                     |                                                                                      aCTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACaaaaac                                                                                  >  2:345816/1‑89 (MQ=255)            ttACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGa                                                                      >  1:593031/1‑90 (MQ=255)             tACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGAc                                                                     <  2:60763/90‑1 (MQ=255)             tACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGAc                                                                     <  1:460805/90‑1 (MQ=255)                       ggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCaa                                                           <  1:152728/90‑1 (MQ=255)                                   tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt                                               <  2:593031/90‑1 (MQ=255)                                   tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt                                               <  2:122676/90‑1 (MQ=255)                                         cAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCtt                                          <  1:493690/90‑1 (MQ=255)                                          aaTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTaa                                        >  1:360110/1‑90 (MQ=255)                                            tGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGa                                      >  1:137871/1‑90 (MQ=255)                                                            gCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAAc                      >  2:457168/1‑90 (MQ=255)                                                             ccAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACa                     >  1:329133/1‑90 (MQ=255)                                                                ggACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt                                               <  2:545823/61‑1 (MQ=255)                                                                ggACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt                                               >  1:545823/1‑61 (MQ=255)                                                                  aCCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACaaaaaa                <  2:32384/90‑1 (MQ=255)                                                                     tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag             >  2:216222/1‑90 (MQ=255)                                                                     tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag             >  1:216701/1‑90 (MQ=255)                                                                     tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag             >  1:515175/1‑90 (MQ=255)                                                                     tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag             >  1:413979/1‑90 (MQ=255)                                                                      gCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAgg            >  1:296462/1‑90 (MQ=255)                                                                           aaGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGa       >  2:30560/1‑90 (MQ=255)                                                                           aaGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGa       >  2:516633/1‑90 (MQ=255)                                                                              aaTTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGa    <  1:345816/90‑1 (MQ=255)                                                                               aTTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGAt   >  2:374179/1‑90 (MQ=255)                                                                                ttAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATg  >  1:245946/1‑90 (MQ=255)                                                                                     |                                                                                      ACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG  >  NZ_CP009273/1613664‑1613833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑