Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,749,544	1	.	A	58.3%	12.6 / 15.3	12	coding (700/1605 nt)	ydhS	conserved hypothetical protein with FAD/NAD(P)‑binding domain
Reads supporting (aligned to +/- strand):  ref base . (0/5);  new base A (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 = 6.21e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TCGTTTTTCACCGCGATAACGCAAGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTATT  >  W3110S.gb/1749518‑1749604                            |                                                             tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTa                          >  1:2892388/1‑64 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:1446766/1‑65 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:2456726/1‑65 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:2538265/1‑65 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:2816439/1‑65 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:679155/1‑65 (MQ=255) tcgtTTTTCACCGCGATAACGCAAGTGAAAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTAt                         >  1:690041/1‑65 (MQ=255)                       aaGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTAtt  <  1:1028434/65‑1 (MQ=255)                       aaGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTAtt  <  1:2131979/65‑1 (MQ=255)                       aaGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTAtt  <  1:2417320/65‑1 (MQ=255)                       aaGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTAtt  <  1:2589964/65‑1 (MQ=255)                       aaGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTAtt  <  1:2884152/65‑1 (MQ=255)                            |                                                             TCGTTTTTCACCGCGATAACGCAAGTG‑AAAAGCTAAATATCACGTTGTTGTCGCGCACGGGTATTTTACCCGAAGCCGATTTCTATT  >  W3110S.gb/1749518‑1749604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑