Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	699,632	0	T	G	58.3%	3.2 / 12.0	12	V78G (GTA→GGA)	nagE	PTS N‑acetyl glucosamine transporter subunit IIABC
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (7/0);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCATCGGTGTGGCATCCAGCTGGTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAACATGGGTGTACTGGCGGG  >  NZ_CP009273/699569‑699701                                                                |                                                                      ccATCGGTGTGGCATCCAGCTGGTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGa                                             <  2:581830/90‑1 (MQ=255)   aTCGGTGTGGCATCCAGCTGGTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGGGCGGGAGGGTACTTTTTGTTTAACAAAACGATg                                           >  2:511279/1‑90 (MQ=255)           ggCATCCAGCTGGTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGGGGGGGAGGGTACTTTTTGTTTAACAAAACGGTGGGGGCCAt                                   >  2:14831/1‑90 (MQ=255)                      ggTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGGGCGGGAGGTTACTTTTTGTTTAACAAAACGATGGGGACCATCAACCCCGaaa                        >  2:217112/1‑90 (MQ=255)                      ggTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGGGCGGGAGGGTACTTTTTGTTAACCAAAACGATGGGGACCCTCAACCCCGaaa                        >  2:90468/1‑90 (MQ=255)                           aaaGACAGCGCTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAAc                   <  1:90468/90‑1 (MQ=255)                              gACAGCGCTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAACATg                <  2:157728/90‑1 (MQ=255)                                   cgcTGGTGCGGCGGCGCTGGCGGGGGCGGGAGGGTTCTTTTTGTTTACCAAAACGATGGGGGCCCTCAACCCACAAAATAAAAAGGgggt           >  2:281411/1‑90 (MQ=255)                                     cTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAACATGGGTGTAc         <  2:590925/90‑1 (MQ=255)                                       ggTGCGGCGGCGCTGGCGGGGGCGGGGGGGTTCTTTTTGTTTAACAAAACGGTGGGGGCCCTCAACCCCAAAAATAAAAAGGGGGTACTg       >  1:226273/1‑90 (MQ=255)                                           cggcggcgCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAACATGGGTGTACTGGCgg   <  1:328004/90‑1 (MQ=255)                                            ggcggcgCTGGCGGGGGCGGGAGGGTTCTTTTTGTTTACCCAAACGGGGGGGGCCCTCAACCCCGAAAATAAAAAGGGGGTGATGGCggg  >  1:139429/1‑90 (MQ=255)                                                                |                                                                      CCATCGGTGTGGCATCCAGCTGGTCGAAAGACAGCGCTGGTGCGGCGGCGCTGGCGGGTGCGGTAGGTTACTTTGTGTTAACCAAAGCGATGGTGACCATCAACCCAGAAATTAACATGGGTGTACTGGCGGG  >  NZ_CP009273/699569‑699701

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑