Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_012967	3,875,625:1	+T	100%	intergenic (‑59/+294)	glmU ← / ← atpC	bifunctional UDP‑N‑acetylglucosamine diphosphorylase/glucosamine‑1‑phosphate N‑acetyltransferase GlmU/F0F1 ATP synthase subunit epsilon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_012967	3,875,625	1	.	T	100.0%	15.6 / NA	7	intergenic (‑59/+294)	glmU/atpC	bifunctional UDP‑N‑acetylglucosamine diphosphorylase/glucosamine‑1‑phosphate N‑acetyltransferase GlmU/F0F1 ATP synthase subunit epsilon
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (4/3);  total (4/3)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑TTTTTTTCATCGTGAAATGGACAGAGGATA  >  NC_012967/3875591‑3875655                                    |                               aCGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑t                               >  1:595072/1‑36 (MQ=255)  gaaaTTTAACCCGCTTCACCTTGAAAAAACTACA‑tt                              <  1:885242/34‑1 (MQ=37)  cGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑tt                              <  1:590454/36‑1 (MQ=255)          aaCCGCTTCACCTTGAAAAAACTACA‑ttttttttca                      >  2:21200/1‑33 (MQ=255)             cGCTTCACCTTGAAAAAACTACATTTTTTTTCATCg                    >  1:411427/1‑36 (MQ=38)              gCTTCACCTTGAAAAAACTACATTTTTTTTCATCGt                   <  2:704249/36‑1 (MQ=37)              gCTTCACCTTGAAAAAACTACATTTTTTTTCATCGt                   <  1:173527/36‑1 (MQ=37)              ccTTCACCTTGAAAAAACTACATTTTTTTTCATCGt                   >  1:758935/2‑36 (MQ=37)                       tGAAAAAACTACATTTTTTTTCATCGTGAAATGGAc          <  2:652296/36‑1 (MQ=37)                            aaaCTACATTTTTTTTCATCGTGAATTGGACAGAgg     >  1:562490/1‑36 (MQ=25)                               cTACATTTTTTTTCATCGTGAAATGGACAGAGGATa  >  2:451692/1‑36 (MQ=37)                                    |                               ACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑TTTTTTTCATCGTGAAATGGACAGAGGATA  >  NC_012967/3875591‑3875655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑