Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,500,285	0	A	C	54.5%	6.4 / 12.1	11	V18G (GTA→GGA)	ydcO	BenE family transporter YdcO
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTGTGCAGTGGTGGCTCCGGCGACAATCGCTGCTTGCCAGATTATTGCCGCTGAACTGGCGTAGCCAATTAATACCGCCAGAAACCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCTCGTGCGTTATAGC  >  NZ_CP009273/1500212‑1500358                                                                          |                                                                          ttGTGCAGTGGTGGCTCCGGCGACAATCGCTGCTTGCCAGATTATTGCCGCTGAACTGGCGTAGCCAATTAATACCGCCAGAAACCCCGc                                                           >  1:755476/1‑90 (MQ=255)   gtgCAGTGGTGGCTCCGGCGACAATCGCTGCTTGCCAGATTATTGCCGCTGAACTGGCGTAGCCAATTAATACCGCCAGAAACCCCGCCa                                                         >  1:486468/1‑90 (MQ=255)                  cGGCGACAATCGCTGCTTGCCAGATTATTGCCGCTGAACTGGCGTAGCCAATTAATACCGCCAGAAACCCCGCCAGTAGCGTGGGTggag                                          >  1:885067/1‑90 (MQ=255)                             gctgctTGCCAGATTTTTGCCGCTGAACGGGCGTAGCAAATTAATCCCGCCAAAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAAc                               <  2:85005/90‑1 (MQ=255)                                        gATTATTGCCGCTGAACTGGCGTAGCCAATTAATAc                                                                          <  1:337599/36‑1 (MQ=255)                                        gATTATTGCCGCTGAACTGGCGTAGCCAATTAATAc                                                                          >  2:337599/1‑36 (MQ=255)                                             ttGCCGCTGAACGGGCGTAGCAAATTAATCCCCCCAAAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCt               <  2:852587/90‑1 (MQ=255)                                             ttGCCGCTAAACGGGGGTAGCCAATTAATCCCGCCAGAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCt               <  2:22451/90‑1 (MQ=255)                                               gCCGTTGAACGGGCGTAGCAAATTAACCCCGCCAAAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCTCg             <  2:780362/90‑1 (MQ=255)                                                          ggCGTACCCAATTAATCCCCCCAAAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCTCGTGCGTTATAGc  <  2:486468/90‑1 (MQ=255)                                                          ggCGTACCAAATAAACCCCGCAAAAACCCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCTCGTGCGTTATAGc  <  2:885067/90‑1 (MQ=255)                                                                          |                                                                          TTGTGCAGTGGTGGCTCCGGCGACAATCGCTGCTTGCCAGATTATTGCCGCTGAACTGGCGTAGCCAATTAATACCGCCAGAAACCCCGCCAGTAGCGTGGGTGGAGGAATAGAAAACAGACGCATAGTCACCTCGTGCGTTATAGC  >  NZ_CP009273/1500212‑1500358

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑