Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,410	T→A	pseudogene (543/687 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	3,824,410	0	T	A	100.0%	116.7 / NA	37	pseudogene (543/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (19/18);  total (19/18)

GTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCA  >  W3110S.gb/3824357‑3824456                                                      |                                               gTCGGTGTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag                                         <  1:3056644/61‑1 (MQ=255) gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag                                         <  1:1275699/61‑1 (MQ=255)    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                                      >  1:155730/4‑61 (MQ=255)    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                                      >  1:2824012/4‑61 (MQ=255)    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                                      >  1:3214221/4‑61 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                          >  1:4696932/3‑56 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                          >  1:4379667/3‑56 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:1067150/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:2826412/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:2477968/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:3410809/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:4305374/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:1964145/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:1754311/3‑62 (MQ=255)     gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                    >  1:1459380/3‑62 (MQ=255)        ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc                                 <  1:2123176/62‑1 (MQ=255)              aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                            >  1:404513/1‑61 (MQ=255)                 gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                        >  1:2925199/3‑62 (MQ=255)                       caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                   <  1:3773994/58‑1 (MQ=255)                       caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                   <  1:3222400/58‑1 (MQ=255)                            tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                <  1:3314338/43‑1 (MQ=255)                            tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                <  1:1117053/43‑1 (MQ=255)                            tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                <  1:2656005/43‑1 (MQ=255)                             gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                <  1:1545937/42‑1 (MQ=255)                                   tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg      >  1:2714023/1‑62 (MQ=255)                                   tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg      >  1:3356351/1‑62 (MQ=255)                                   tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg      >  1:222155/1‑62 (MQ=255)                                   tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg      >  1:1168523/1‑62 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg        <  1:3246493/56‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg        <  1:2332840/56‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg        <  1:4305360/56‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg        <  1:2199705/56‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGca  <  1:2787999/62‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGca  <  1:2338823/62‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGca  <  1:485720/62‑1 (MQ=255)                                       aTACGTTGAAGACTCAGCCGCAGAGACCGACAAGAACGTAGTGATGACCGAAGACGGGCGca  <  1:4051882/62‑1 (MQ=255)                                             tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg        <  1:996947/50‑1 (MQ=255)                                                      |                                               GTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCA  >  W3110S.gb/3824357‑3824456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑