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%	234.4 / NA	72	pseudogene (507/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (36/36);  total (36/36)

GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824342‑3824434                                 |                                                             gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATActt                                    <  1:2203861/59‑3 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2601794/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:1999957/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2212399/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2312875/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2316446/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:758566/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:240887/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2517901/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:1067019/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:992770/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:286509/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2943398/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:621762/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:3071721/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:60478/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:526826/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:342116/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:375279/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:1842413/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:889302/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:1614660/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:1652320/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:801929/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:800760/59‑1 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:76619/59‑1 (MQ=255)       gctgTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:5040/4‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:778138/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:454230/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:752554/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:405409/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:2346688/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:3051156/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:1677756/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:2513316/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:1630998/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:2112518/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:2744166/1‑65 (MQ=255)       gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:2924726/1‑65 (MQ=255)               tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                    <  1:2999632/45‑1 (MQ=25)                           aaaCGGTGAAGCATTTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2308537/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:846169/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2675516/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:3022367/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2402396/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:188916/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:1288207/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:125598/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:939163/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:666524/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2343414/2‑63 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:1760280/2‑63 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:821167/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:866328/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:2597848/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:1755263/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:1186184/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:1222828/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:1699489/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:2341791/64‑1 (MQ=255)                            aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:332111/64‑1 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:2348629/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:2339913/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1798565/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:384983/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1748284/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:306879/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1503753/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1320493/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1295806/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:1290353/1‑65 (MQ=255)                             aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  >  1:3073809/1‑65 (MQ=255)                                 |                                                             GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824342‑3824434

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: ‑