Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,632,893	1	.	A	58.3%	61.7 / 55.7	36	coding (897/1233 nt)	nadR	bifunctional DNA‑binding transcriptional repressor and NMN adenylyltransferase
Reads supporting (aligned to +/- strand):  ref base . (15/0);  new base A (0/21);  total (15/21)
Fisher's exact test for biased strand distribution p-value = 1.80e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.97e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAGG  >  W3110S.gb/4632880‑4632945               |                                                     ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGGATTTATCGATACCGATTTTGTCACCACTCa    <  1:29170/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1088717/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:82665/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:800972/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:787472/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:445587/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:306949/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2474743/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2350111/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2298421/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2067502/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2043950/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:2041861/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1845388/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:179225/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1698063/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1408691/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1359023/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1034149/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1321363/65‑1 (MQ=255) ttGATTTTGCGGTGAAAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCa    <  1:1138938/65‑1 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:95664/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:894864/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:891280/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:839765/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:1243378/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:699556/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:128204/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:416499/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:415816/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:1292543/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:253347/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:2435942/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:2280979/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAgg  >  1:208717/1‑65 (MQ=255)  tGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGACACCACTCAg   >  1:1882002/1‑64 (MQ=255)               |                                                     TTGATTTTGCGGTG‑AAATATGCCAATAAAGTGGCATTTATCGATACCGATTTTGTCACCACTCAGG  >  W3110S.gb/4632880‑4632945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑