Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,281,658	2 bp→GC	intergenic (+178/‑172)	agaA → / → agaS	predicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,281,658	0	A	G	83.3%	120.5 / 15.9	54	intergenic (+178/‑173)	agaA/agaS	predicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
Reads supporting (aligned to +/- strand):  ref base A (0/9);  new base G (45/0);  total (45/9)
Fisher's exact test for biased strand distribution p-value = 1.88e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01
*	W3110S.gb	3,281,659	0	T	C	83.3%	121.2 / 14.9	54	intergenic (+179/‑172)	agaA/agaS	predicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
Reads supporting (aligned to +/- strand):  ref base T (0/9);  new base C (45/0);  total (45/9)
Fisher's exact test for biased strand distribution p-value = 1.88e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGCGCCGCATCCAGCAATCCCTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTTCT  >  W3110S.gb/3281624‑3281703                                   ||                                             tacgccgcTTCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:373444/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2924411/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2456486/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1087815/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2514934/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2559811/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2609452/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2628142/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2670605/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:267937/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2706942/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2720210/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2803769/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2468124/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2924688/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:432178/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:438813/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:452641/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:613994/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:691624/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:901810/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:951388/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:959845/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:995483/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1719749/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1122987/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1194326/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1218626/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1227912/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1363861/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1459735/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1480099/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1522848/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1639025/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1708469/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2439088/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:177836/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2395609/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:1935413/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:198629/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2217707/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2188143/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2016765/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGATCACAGATTTc                    >  1:2003377/3‑62 (MQ=255) tacgccgcATCCAGCAATCCCTTTTACTTCCCTTGCCTTTTCTTTCAACGAT‑ACAGATTTCg                   >  1:2591300/3‑62 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:1900224/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:1989867/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:357335/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:662131/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:1206344/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:245807/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:114514/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTtct  <  1:2785105/62‑1 (MQ=255)                   cccTTTTGCTTCCTTTATCTTTTCATTCAACGATCAAAAATTTCGTTTTATTTCTTTTTtct  <  1:2632702/62‑1 (MQ=255)                                   ||                                             TGCGCCGCATCCAGCAATCCCTTTTGCTTCCTTTATCTTTTCTTTCAACGATCACAAATTTCGTTTTATTTCTTTTTTCT  >  W3110S.gb/3281624‑3281703

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: ‑