Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,248,409	A→C	K3T (AAA→ACA)	BW25113_RS16135 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,248,409	0	A	C	100.0%	107.9 / NA	32	K3T (AAA→ACA)	BW25113_RS16135	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (19/13);  total (19/13)

ACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAG  >  NZ_CP009273/3248326‑3248494                                                                                    |                                                                                      aCGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAAtt                                                                                 >  1:720420/1‑90 (MQ=255)     tGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGcc                                                                             >  1:285629/1‑90 (MQ=255)      ggTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCa                                                                            >  2:474235/1‑90 (MQ=255)      ggTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCa                                                                            >  1:854463/1‑90 (MQ=255)       gTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCaa                                                                           >  2:866349/1‑90 (MQ=255)              aTTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAgcgc                                                                    <  1:474235/90‑1 (MQ=255)                     aCTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCgg                                                             >  2:249834/1‑90 (MQ=255)                       tGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTg                                                           <  2:720420/90‑1 (MQ=255)                        gcgcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGa                                                          >  2:796736/1‑90 (MQ=255)                        gcgcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGa                                                          >  1:751681/1‑90 (MQ=255)                        gcgcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGa                                                          >  2:272512/1‑90 (MQ=255)                                tGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCgtg                                                  <  2:486441/90‑1 (MQ=255)                                       aGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGa                                           >  2:636612/1‑90 (MQ=255)                                           ttGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGa                                       >  1:588132/1‑90 (MQ=255)                                                 gTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGc                                 >  2:657604/1‑90 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCAc                           >  1:372065/1‑86 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCAc                           <  2:372065/86‑1 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGcc                       >  2:791852/1‑90 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGcc                       >  2:65741/1‑90 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGcc                       >  1:218945/1‑90 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGcc                       >  1:70565/1‑90 (MQ=255)                                                           ttttACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGcc                       >  1:186718/1‑90 (MQ=255)                                                                    gagaTGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAAtttt              <  2:380359/90‑1 (MQ=255)                                                                    gagaTGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAAtttt              <  2:596047/90‑1 (MQ=255)                                                                    gagaTGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTAGTGGCGAAAGAACCTGCTCGCACCGCCAAAAAtttt              <  2:21500/90‑1 (MQ=255)                                                                       atgatgatgAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGc           <  2:12710/90‑1 (MQ=255)                                                                       atgatgatgAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGc           <  1:511627/90‑1 (MQ=255)                                                                       atgatgatgAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGc           <  1:249834/90‑1 (MQ=255)                                                                         gatgatgaGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTa         <  2:751681/90‑1 (MQ=255)                                                                          atgatgaGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTAt        <  2:26839/90‑1 (MQ=255)                                                                            gatgaGTACAAAGTTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGa      <  2:808299/90‑1 (MQ=255)                                                                                aGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAagag  >  1:506214/1‑90 (MQ=255)                                                                                    |                                                                                      ACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGGCTATGAAGAG  >  NZ_CP009273/3248326‑3248494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑