Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,362	A→T	pseudogene (495/687 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	3,824,362	0	A	T	100.0%	173.7 / NA	54	pseudogene (495/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/41);  total (13/41)

AAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGC  >  W3110S.gb/3824305‑3824412                                                          |                                                   aaaCGGCAAGCTGAAAACCAACCCGATTAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2163814/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:981310/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:1621117/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:816029/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:645616/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:539493/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2754095/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2734151/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2572717/60‑1 (MQ=255) aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2479939/60‑1 (MQ=255)  aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:1457024/59‑1 (MQ=255)  aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2813282/59‑1 (MQ=255)         aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:113007/52‑1 (MQ=255)                         gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                  <  1:2820104/36‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATActt              <  1:2203861/59‑3 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:342116/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:992770/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1614660/59‑1 (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              <  1:1652320/59‑1 (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              <  1:2312875/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:3071721/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2316446/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:240887/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:286509/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1067019/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2212399/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1842413/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:1999957/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2943398/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2517901/59‑1 (MQ=255)                                      gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2601794/59‑1 (MQ=255)                                            gctgTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:5040/4‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2744166/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2346688/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:1630998/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2513316/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:778138/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:752554/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2112518/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:1677756/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:454230/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:405409/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:2924726/1‑65 (MQ=255)                                            gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc  >  1:3051156/1‑65 (MQ=255)                                                    tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt              <  1:2999632/45‑1 (MQ=25)                                                          |                                                   AAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGC  >  W3110S.gb/3824305‑3824412

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: ‑