Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,272,186	0	C	A	55.6%	3.9 / 12.9	9	G352C (GGC→TGC)	bcr	multidrug efflux MFS transporter Bcr
Reads supporting (aligned to +/- strand):  ref base C (3/1);  new base A (0/5);  total (3/6)
Fisher's exact test for biased strand distribution p-value = 4.76e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATC  >  NZ_CP009273/2272116‑2272259                                                                       |                                                                           gACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGcc                                                        >  2:47203/1‑90 (MQ=255)           tcGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATg                                              >  1:407509/1‑90 (MQ=255)                 aTGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTc                                        <  1:47203/90‑1 (MQ=255)                        ttaaaaGGCCGAAAGAAAAAGAAATGCCCCAACAATTCCCCCTATGCAAAAAGGGAGGTTC‑CCTGCCAGCAAAGATGCCGTTCCCGCCat                                 <  2:19707/87‑1 (MQ=255)                                               aTGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGa          >  1:17743/1‑90 (MQ=255)                                                 gccccAAAATTTCCCCCTATCCAAAAACGAAAGTTC‑CCGCCCAGCAAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGAcc        <  2:255924/87‑1 (MQ=255)                                                     caaaaaTTCCCCCTTACCAAAAACGGAAAGTTCCCCCCCAGCAAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGcc     <  2:407509/90‑1 (MQ=255)                                                      aacaaTTCCCCCTACCCAAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCAt   <  2:204509/90‑1 (MQ=255)                                                       aaatttGCCCCTATGCAAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATc  <  1:79234/86‑1 (MQ=255)                                                                       |                                                                           GACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATC  >  NZ_CP009273/2272116‑2272259

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑