Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,541,664	G→A	E129K (GAA→AAA)	crr →	glucose‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,541,664	0	G	A	100.0%	332.7 / NA	89	E129K (GAA→AAA)	crr	glucose‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (0/89);  total (0/89)

GCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAA  >  W3110S.gb/2541657‑2541722        |                                                           gcttctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1077617/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:407193/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:590048/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:589794/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:588104/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:523011/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:522820/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:491594/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:480584/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:480579/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:478264/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:460785/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:437986/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:598769/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:392127/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:370435/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:367068/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:346491/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:271643/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:236157/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:168701/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:163616/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1591604/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:814429/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:995804/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:909479/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:889701/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:881728/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:869260/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:857827/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:857183/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:854408/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:842560/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:816548/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1581222/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:814010/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:804227/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:782092/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:77498/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:705656/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:692979/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:649118/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:635541/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:604528/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1115499/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1227158/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1218785/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:121454/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1201769/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1195745/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1171961/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:11410/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1132996/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1121933/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1118375/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1262632/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1114684/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1081305/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1072602/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1068642/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1042820/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1042395/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1035872/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1029556/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1027241/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1024845/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1004130/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1503702/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:150256/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1482898/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1534462/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1457655/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:145102/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1447784/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1439576/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1424023/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1416208/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1415194/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1414712/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1414278/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1410297/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1395358/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1353256/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1346074/66‑1 (MQ=255) gctgctGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1301282/66‑1 (MQ=255) gctgccGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:460624/66‑1 (MQ=255)  ctgctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1271308/65‑1 (MQ=255)  ctgctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:861565/65‑1 (MQ=255)   tgctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCaa  <  1:1552954/64‑1 (MQ=255)        |                                                           GCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAA  >  W3110S.gb/2541657‑2541722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑