Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,918,949	0	A	C	53.8%	12.1 / 14.0	13	G15G (GGT→GGG)	mnmG	tRNA uridine‑5‑carboxymethylaminomethyl(34) synthesis enzyme MnmG
Reads supporting (aligned to +/- strand):  ref base A (5/1);  new base C (0/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: Frequency below/above cutoff threshold.

GTCGATATTGTGTGTCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGTGATTGCCTCGCATAACGC  >  NZ_CP009273/3918874‑3919014                                                                            |                                                                  gtCGATATTGTGTGTCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAatgat                                                     >  1:189337/1‑90 (MQ=255) gtCGATATTGTGTGTCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAatgat                                                     >  1:47218/1‑90 (MQ=255)           tgtgtCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCa                                           >  1:312918/1‑90 (MQ=255)            gtgtCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCaa                                          >  1:409470/1‑90 (MQ=255)                   aaGGAGAGTGTGTAAACCCATACGCGCCGCGGCCTTCGCGGCCCGGGTGCAGGGATGCCCCCCGCCAATGATGATGACGTCAAAAGGATc                                   <  1:217479/90‑1 (MQ=255)                   aaGCAGATTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATc                                   <  1:167368/90‑1 (MQ=255)                   aaGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATc                                   <  2:17787/90‑1 (MQ=255)                   aaGCAGAGTCTGTCGCCCAATACGCGCCGCGGCCATCGCGGCCTGGGTGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATc                                   <  2:378268/90‑1 (MQ=255)                         agTCTGTTGCCCCATACGCGCCGCGGCCATCGCGGCCTGGGTGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATa                             <  2:339840/90‑1 (MQ=255)                                  aCCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGt                    >  1:144534/1‑90 (MQ=255)                                         cgcgCCGCGGCCATCGCGGCCTCGGTGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGTGATTGcc             <  2:129129/90‑1 (MQ=255)                                          gcgcCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGTGATTGCCt            <  1:36129/90‑1 (MQ=255)                                                    cagcgcgGCCTGGGGGCCTGCATGCCCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGTGATTGCCTCGCATAAcgc  <  2:47218/87‑1 (MQ=255)                                                                            |                                                                  GTCGATATTGTGTGTCAAAAGCAGAGTCTGTTGACCCATACGCGCCGCGGCCATCGCGGCCTCGGTGCCTGCATGACCCCCGCCAATGATGATGACGTCAAAAGGATCCGGATAAAACATGGTGATTGCCTCGCATAACGC  >  NZ_CP009273/3918874‑3919014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑