Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,374	C→T	pseudogene (507/687 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	3,824,374	0	C	T	100.0%	126.1 / NA	40	pseudogene (507/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/13);  total (27/13)

GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAA  >  W3110S.gb/3824317‑3824430                                                          |                                                         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                                 >  1:2122182/1‑61 (MQ=255)                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                 >  1:3918299/1‑61 (MQ=255)                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                 >  1:3750738/1‑61 (MQ=255)                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                 >  1:3596056/1‑61 (MQ=255)                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                 >  1:2954390/1‑61 (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                >  1:4379667/3‑56 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                >  1:4696932/3‑56 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:1067150/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:4305374/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:1459380/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:3410809/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:1754311/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:1964145/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:2826412/3‑62 (MQ=255)                                             gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc          >  1:2477968/3‑62 (MQ=255)                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc       <  1:2123176/62‑1 (MQ=255)                                                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa  >  1:404513/1‑61 (MQ=255)                                                          |                                                         GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAA  >  W3110S.gb/3824317‑3824430

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: ‑