Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,537	+G	pseudogene (670/687 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	3,824,533	1	.	G	100.0%	140.1 / NA	41	pseudogene (666/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (22/19);  total (22/19)

CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACTG  >  W3110S.gb/3824468‑3824598                                                                   |                                                                  cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggg                                                              <  1:2127732/71‑2 (MQ=255) cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                                               >  1:242916/1‑70 (MQ=255)    gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggga                                                             <  1:3519562/69‑3 (MQ=255)       aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                                          <  1:596697/70‑1 (MQ=255)          gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaatc                                                      <  1:901054/71‑1 (MQ=255)             gAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt                                                   <  1:1373422/71‑1 (MQ=255)               aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                                                 >  1:458648/1‑71 (MQ=255)                ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                                                 >  1:4008695/1‑70 (MQ=255)                ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                                                 >  1:2408867/1‑70 (MQ=255)                ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt                                                <  1:2993067/71‑1 (MQ=255)                   gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATTGAATCCATTGTAGc                                             <  1:3966776/71‑1 (MQ=255)                   gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc                                             <  1:1402522/71‑1 (MQ=255)                   gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc                                             <  1:2351030/71‑1 (MQ=255)                        gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt                                                <  1:2911125/63‑1 (MQ=255)                         ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa                                       <  1:2308181/71‑1 (MQ=255)                           cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                                      >  1:2107674/1‑70 (MQ=255)                           cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                                      >  1:1402946/1‑70 (MQ=255)                           cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                                      >  1:4490660/1‑70 (MQ=255)                            aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa                                    <  1:3302995/71‑1 (MQ=255)                               cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc                                 >  1:2171336/1‑71 (MQ=255)                               cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc                                 >  1:1451573/1‑71 (MQ=255)                                 tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg                                  <  1:4195410/68‑1 (MQ=255)                                 tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg                                  <  1:1593381/68‑1 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAg                                              >  1:1555145/1‑54 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa                                       >  1:4348033/1‑61 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc                              >  1:970107/1‑70 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc                              <  1:1970565/70‑1 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg                                  >  1:184600/1‑66 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg                             >  1:3317656/1‑71 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg                             >  1:2406073/1‑71 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg                             >  1:2492466/1‑71 (MQ=255)                                   aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg                             >  1:126034/1‑71 (MQ=255)                                           cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa                     >  1:428130/1‑71 (MQ=255)                                           cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa                       <  1:3868553/69‑1 (MQ=255)                                              accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt                   >  1:3487983/3‑70 (MQ=255)                                               ccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa                 <  1:3234868/70‑1 (MQ=255)                                                cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt                >  1:4398766/1‑71 (MQ=255)                                                 ttgttgGCGCTGGCCCGAGGGGGAATCGAATGCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt                >  1:641072/1‑70 (MQ=255)                                                 ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa                     >  1:4343178/1‑65 (MQ=255)                                                 ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt               >  1:1845131/1‑71 (MQ=255)                                                    ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtttt             <  1:2529031/70‑1 (MQ=255)                                                    ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACCGAtttt             <  1:2772891/70‑1 (MQ=255)                                                              cccGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACtg  <  1:1429027/71‑1 (MQ=255)                                                              cccGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACtg  <  1:3516068/71‑1 (MQ=255)                                                                   |                                                                  CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACTG  >  W3110S.gb/3824468‑3824598

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: ‑