Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,260,970	T→C	intergenic (+13/‑243)	tdcR → / → BW25113_RS16190	transcriptional activator TdcR/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,260,970	0	T	C	91.7%	33.1 / NA	12	intergenic (+13/‑243)	tdcR/BW25113_RS16190	transcriptional activator TdcR/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (6/5);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGATTAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCTCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATCGCCGCGATAAGG  >  NZ_CP009273/3260891‑3261038                                                                                |                                                                     aTTGATTAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGcgac                                                            >  1:514305/1‑90 (MQ=255) aTTGATTAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTT‑CATAAATTTTTCTCCCCTCCTAAGcgacg                                                           >  1:514245/1‑90 (MQ=255)       tAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAg                                                      <  1:154020/90‑1 (MQ=255)       tAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAg                                                      <  1:195865/90‑1 (MQ=255)         aCGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCa                                                    >  2:118921/1‑90 (MQ=255)              aaCTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTtg                                               >  2:381350/1‑90 (MQ=255)                          tctGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATca                                   >  1:12204/1‑90 (MQ=255)                                           ttGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCt                  >  1:364828/1‑90 (MQ=255)                                                   gCAATCGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATcgccg          <  1:354629/90‑1 (MQ=255)                                                        cGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATCGCCGCGATa     <  2:157725/90‑1 (MQ=255)                                                        cGTTTTCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATCGCCGCGATa     <  2:364828/90‑1 (MQ=255)                                                           tttCCATAAATTCTTCTCCCCCCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATCGCCGCGATAAgg  >  2:360975/1‑90 (MQ=255)                                                                                |                                                                     ATTGATTAACGTCAACTTTTTCTCTTCTGACAGGACGTCATTTTGTGAATGCAATCGTTTTCCATAAATTCTTCTCCCCTCATAGGCGACGAATAGCATTTTGTGTTGAGGATCACAAAACGAATAATTGCTGATCGCCGCGATAAGG  >  NZ_CP009273/3260891‑3261038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑