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	90.9%	29.7 / ‑3.1	11	K3T (AAA→ACA)	BW25113_RS16135	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (8/2);  total (9/2)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

ACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGG  >  NZ_CP009273/3248326‑3248484                                                                                    |                                                                            aCGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAAtt                                                                       >  2:104034/1‑90 (MQ=255) aCGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAAtt                                                                       <  2:39788/90‑1 (MQ=255)  cGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTg                                                                      >  2:122559/1‑90 (MQ=255)      ggTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCa                                                                  >  2:187024/1‑90 (MQ=255)      ggTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCa                                                                  >  2:195197/1‑90 (MQ=255)      ggTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCa                                                                  >  2:363545/1‑90 (MQ=255)         tGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCaaaa                                                               <  1:251985/90‑1 (MQ=255)                        gcgcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGa                                                >  1:267953/1‑90 (MQ=255)                        gcgcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGa                                                >  1:2851/1‑90 (MQ=255)                          gcgcTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAg                                              >  1:150426/1‑90 (MQ=255)                                                                      gatgatgatGAGTACAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTgg  >  2:365061/1‑90 (MQ=255)                                                                                    |                                                                            ACGCTGGTTGCCGATTCCCCACTGCGCGCTTTGCTGATAGATTTGCCTGTCTAGTTGTTTTTACAGGGAGATGATGATGAGTAAAAAATTGGCCAAAAAGCGCCAGCCGGTGAAGCCCGTGGTGGCGAAAGAACCTGCTCGCACCGCCAAAAATTTTGG  >  NZ_CP009273/3248326‑3248484

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑