Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,681,729	0	A	T	52.9%	‑5.8 / 22.0	17	S71C (AGC→TGC)	yphH	predicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (0/8);  new base T (0/9);  total (0/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TATTGACGATGAAAGCCAGACGCGCGGGCATAGTAGCGGTACATGGCTGATTGCGCCGGAAGGTGACTGG  >  W3110S.gb/2681695‑2681764                                   |                                    tatTGACGATGAAAGCCAGACGCGCGGGCATAGTAGCGGTa                               <  1:4411730/41‑1 (MQ=255) tatTGACGATGAAAGCCAGACGCGCGGGCATAGTAGCGGTa                               <  1:413377/41‑1 (MQ=255)   ttGACGATGAAAGCCAGACGCGCGGGCATAGTAGc                                   <  1:1084344/35‑1 (MQ=255)   ttGACGATGAAAGCCAGACGCGCGGGCATAGTAGc                                   <  1:981104/35‑1 (MQ=255)   ttGACGATGAAAGCCAGACGCGCGGGCATAGTAGc                                   <  1:808316/35‑1 (MQ=255)   ttGACGATGAAAGCCAGACGCGCGGGCATAGTAGc                                   <  1:2837596/35‑1 (MQ=255)         aTGAAAGCCAGACGCGCGGGCATAGTAGCGGTACATGGCTGATTGCGCCGGAAGGTGACTgg  <  1:1549326/62‑1 (MQ=255)          tGAAAGCCAGACGCGCGGGCATAGTAGCGGTACATGGCTGATTGCGCCGGAAGGTGACTgg  <  1:368409/61‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3829324/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3864162/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3905409/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3910738/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:4168383/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3348297/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:2533924/57‑1 (MQ=255)           gAAAGCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:162474/57‑1 (MQ=255)           gAAACCCAGACGCGCGGGCATAGTTGCGGTACATGGCTGATTGCGCCGGAAGGTGAc     <  1:3538148/57‑1 (MQ=255)                                   |                                    TATTGACGATGAAAGCCAGACGCGCGGGCATAGTAGCGGTACATGGCTGATTGCGCCGGAAGGTGACTGG  >  W3110S.gb/2681695‑2681764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑