Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,338,358	0	G	T	60.0%	‑2.5 / 10.8	10	G95C (GGT→TGT)	rpoN	RNA polymerase factor sigma‑54
Reads supporting (aligned to +/- strand):  ref base G (2/2);  new base T (3/3);  total (5/5)
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
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGT  >  NZ_CP009273/3338307‑3338407                                                    |                                                  aTGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTgacgac             >  1:379490/1‑90 (MQ=255)         agagCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGcc     <  1:442823/90‑1 (MQ=255)           agCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCgg   <  2:279140/90‑1 (MQ=255)            gCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGt  >  2:94646/1‑90 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      >  1:200291/1‑50 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      >  1:360412/1‑50 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      >  1:369531/1‑50 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      <  2:200291/50‑1 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      <  2:360412/50‑1 (MQ=255)                                                cGCTTGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc      <  2:369531/50‑1 (MQ=255)                                                    |                                                  ATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGT  >  NZ_CP009273/3338307‑3338407

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑