Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_012967	3,483,047	C→A	100%	R455S (CGC→AGC)	malT →	HTH‑type transcriptional regulator MalT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_012967	3,483,047	0	C	A	100.0%	23.6 / ‑6.7	10	R455S (CGC→AGC)	malT	HTH‑type transcriptional regulator MalT
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (6/3);  total (7/3)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATC  >  NC_012967/3483026‑3483077                      |                               cACGCAGAATTTAACGCTCTGAGCGCCCAGGTGGCg                  <  1:563827/36‑1 (MQ=39)  aCGCAGAATTTAACGCTCTGAGCGCCCAGGTGGCGa                 >  2:511103/1‑36 (MQ=39)   cGCAGAATTTAACGCTCTGAGCGCCCAGGTGGCGAt                <  2:641408/36‑1 (MQ=39)    gCAGAATTTAACGCTCTGAGCGCCCAGGTGGCGAtt               >  1:46547/1‑36 (MQ=39)     cAGAATTTAACGCTCTGAGCGCCCAGGTGGCGATTa              <  1:967725/36‑1 (MQ=39)        aaTTTAACGCTCTGAGCGCCCAGGTGGCGATTAACg           >  1:471482/1‑36 (MQ=38)                gCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAAt   >  2:749977/1‑36 (MQ=255)                gCTCTGAGCGCCCAGGTGGCGATTAACGATGGTAAt   >  2:519355/1‑36 (MQ=38)                 ctctGAGCGCCCAGGTGGCGATTAACGATGGTCATc  >  2:215291/1‑36 (MQ=37)                 ctctGAGCGCCCAGGTGGCGATTAACGATGGTAATc  >  1:931370/1‑36 (MQ=38)                      |                               CACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATC  >  NC_012967/3483026‑3483077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑