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%	146.8 / NA	45	pseudogene (501/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (32/13);  total (32/13)

AAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGAC  >  W3110S.gb/3824312‑3824425                                                         |                                                          aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:3919510/1‑61 (MQ=255) aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:2561043/1‑61 (MQ=255) aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:2764336/1‑61 (MQ=255) aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:4428260/1‑61 (MQ=255) aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:1254280/1‑61 (MQ=255) aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                       >  1:1252895/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:4547675/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:4417425/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:1502545/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:3245740/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:3015540/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:2903051/1‑61 (MQ=255)      gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                  >  1:2729571/1‑61 (MQ=255)          aCCAACCCGATGACAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:4634284/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:1226047/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:3477025/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:3364905/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:2494547/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:2311555/62‑4 (MQ=255)          aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat                                             <  1:1308102/62‑4 (MQ=255)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa                                                   >  1:4118826/1‑38 (MQ=25)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                            >  1:2954390/1‑61 (MQ=255)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                            >  1:2122182/1‑61 (MQ=255)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                            >  1:3918299/1‑61 (MQ=255)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                            >  1:3750738/1‑61 (MQ=255)                            aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                            >  1:3596056/1‑61 (MQ=255)                                    cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc                    <  1:832095/61‑1 (MQ=255)                                    cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc                    <  1:4182397/61‑1 (MQ=255)                                    cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc                    <  1:2020040/61‑1 (MQ=255)                                              gTCGGTGTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag          <  1:3056644/61‑1 (MQ=255)                                              gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag          <  1:1275699/61‑1 (MQ=255)                                                 ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga       >  1:3214221/4‑61 (MQ=255)                                                 ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga       >  1:155730/4‑61 (MQ=255)                                                 ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga       >  1:2824012/4‑61 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa           >  1:4696932/3‑56 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa           >  1:4379667/3‑56 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:2826412/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:2477968/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:1067150/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:1459380/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:4305374/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:1964145/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:1754311/3‑62 (MQ=255)                                                  gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc     >  1:3410809/3‑62 (MQ=255)                                                     ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc  <  1:2123176/62‑1 (MQ=255)                                                         |                                                          AAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGAC  >  W3110S.gb/3824312‑3824425

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: ‑