Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,368	G→A	pseudogene (501/687 nt)	rph →	ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,824,368	0	G	A	100.0%	132.8 / NA	40	pseudogene (501/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/27);  total (13/27)

GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGC  >  W3110S.gb/3824342‑3824412                           |                                             gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATActt              <  1:2203861/59‑3 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2943398/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:992770/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:889302/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:801929/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:800760/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:76619/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:758566/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:621762/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:60478/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:526826/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:375279/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:342116/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:3071721/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1067019/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:286509/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1614660/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2517901/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1652320/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1842413/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1999957/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2212399/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:240887/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2312875/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2316446/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2601794/59‑1 (MQ=255)       gctgTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:5040/4‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:454230/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:405409/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2346688/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:3051156/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2112518/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:752554/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2513316/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:778138/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:1677756/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2924726/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:1630998/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2744166/1‑65 (MQ=255)               tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2999632/45‑1 (MQ=25)                           |                                             GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGC  >  W3110S.gb/3824342‑3824412

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