Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,280	T→C	pseudogene (413/687 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	3,824,280	0	T	C	100.0%	152.8 / NA	45	pseudogene (413/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/25);  total (20/25)

CGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGC  >  W3110S.gb/3824218‑3824346                                                               |                                                                   cGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgcgc                                                            <  1:4000492/71‑1 (MQ=255)  gTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCt                                                           <  1:948264/71‑1 (MQ=255)  gTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCt                                                           <  1:2347623/71‑1 (MQ=255)   tGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa                                                          <  1:2918163/71‑1 (MQ=255)   tGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa                                                          <  1:2007977/71‑1 (MQ=255)     cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa                                                          >  1:3542391/1‑69 (MQ=255)        cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                      <  1:2903730/70‑1 (MQ=255)        cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                      <  1:2722951/70‑1 (MQ=255)        cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                      <  1:3680688/70‑1 (MQ=255)                tggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                      <  1:1678613/62‑1 (MQ=255)                tggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                      <  1:3088201/62‑1 (MQ=255)                  gtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGa                                            >  1:345809/1‑70 (MQ=255)                            tACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaa                                           <  1:1850892/61‑1 (MQ=255)                              ccGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCt                                >  1:3348090/1‑70 (MQ=255)                              ccGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCt                                >  1:3448768/1‑70 (MQ=255)                                gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaa                             <  1:73250/71‑1 (MQ=255)                                gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGa                              >  1:1386855/1‑70 (MQ=255)                                     gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc                         >  1:1953974/1‑70 (MQ=255)                                        tACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaacc                     >  1:1184112/1‑69 (MQ=255)                                        tACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaacc                     >  1:288363/1‑69 (MQ=255)                                        tACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaacc                     >  1:631206/1‑69 (MQ=255)                                        tACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaacc                     >  1:703337/1‑69 (MQ=255)                                            ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaa                                           <  1:2823520/45‑1 (MQ=255)                                            ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                 >  1:4003532/1‑71 (MQ=255)                                            ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                 >  1:744525/1‑71 (MQ=255)                                              tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                >  1:500426/1‑70 (MQ=255)                                              tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                >  1:3531970/1‑70 (MQ=255)                                              tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa               <  1:958890/71‑1 (MQ=255)                                              tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa               <  1:1187740/71‑1 (MQ=255)                                                ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCACCCCGATGa               >  1:2022755/1‑69 (MQ=255)                                                ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa             <  1:905565/71‑1 (MQ=255)                                                ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa               >  1:2376945/1‑69 (MQ=255)                                                ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa               >  1:1820404/1‑69 (MQ=255)                                                ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa               >  1:830155/1‑69 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaaaa                                         >  1:79925/1‑39 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:3431187/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:2760232/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:4448093/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:454243/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:1830383/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:1485458/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:1395024/69‑1 (MQ=255)                                                    cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg           <  1:1355794/69‑1 (MQ=255)                                                        gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg      >  1:909141/1‑70 (MQ=255)                                                           cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc  <  1:3307811/71‑1 (MQ=255)                                                               |                                                                   CGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGC  >  W3110S.gb/3824218‑3824346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑