Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,807,300	C→T	pseudogene (33/882 nt)	ygaY →	ECK2675:JW5428:b2681; predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,807,300	0	C	T	92.7%	191.9 / 4.5	68	pseudogene (33/882 nt)	ygaY	ECK2675:JW5428:b2681; predicted transporter
Reads supporting (aligned to +/- strand):  ref base C (0/5);  new base T (0/63);  total (0/68)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.15e-01

GGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGG  >  W3110S.gb/2807261‑2807331                                        |                                ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2452978/62‑1 (MQ=255) ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:728833/62‑1 (MQ=255) ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2494528/62‑1 (MQ=255) ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2246350/62‑1 (MQ=255)  gCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:1261786/61‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2590453/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:324766/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2921224/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2838158/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:280023/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2799835/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2719636/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2716275/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:399060/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2572359/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2502590/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2454976/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1044421/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:39295/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2436082/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:489771/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:493959/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:538167/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:53914/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:580558/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:64637/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:647193/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:672736/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:690653/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:720069/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:726536/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:845286/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:923740/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:953951/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2385844/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1052364/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:109918/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1204831/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1391083/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1435284/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1525756/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1674216/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1709495/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1767721/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1773613/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1785259/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1796764/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1816745/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1841177/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1946270/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1890243/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2029207/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2037295/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2201201/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2212106/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2304846/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2326940/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2342733/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2328802/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:233050/49‑1 (MQ=255)                     cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2330889/49‑1 (MQ=255)                        cATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2433431/48‑1 (MQ=255)                         aTTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:775012/47‑1 (MQ=255)                         aTTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2637910/47‑1 (MQ=255)                                  tttATTTTCTGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:885220/38‑1 (MQ=25)                                  tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1389139/38‑1 (MQ=38)                                  tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2353789/38‑1 (MQ=38)                                  tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1837844/38‑1 (MQ=38)                                        |                                GGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGG  >  W3110S.gb/2807261‑2807331

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: ‑