Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,844	A→G	pseudogene (38/48 nt)	rph ←	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,844	0	A	G	100.0%	178.3 / NA	50	pseudogene (38/48 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/25);  total (25/25)

TGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCAT  >  NC_000913/3815722‑3815979                                                                                                                           |                                                                                                                                        tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                         <  2:383817/139‑1 (MQ=255)  gcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTc                                                                                                                        >  2:658211/1‑139 (MQ=255)                  ttCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcga                                                                                                        <  2:1162318/139‑1 (MQ=255)                           cTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCg                                                                                               >  1:563299/1‑139 (MQ=255)                            tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCgg                                                                                              >  2:531972/1‑139 (MQ=255)                             ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg                                                                                             >  2:922386/1‑139 (MQ=255)                             ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg                                                                                             >  2:765097/1‑139 (MQ=255)                               cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCg                                                                                                                       >  1:113938/1‑111 (MQ=255)                               cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCg                                                                                                                       <  2:113938/111‑1 (MQ=255)                               cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGcc                                                                                           >  2:505269/1‑139 (MQ=255)                                  tGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCaga                                                                                        <  1:531972/139‑1 (MQ=255)                                        ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                      <  1:1351192/119‑1 (MQ=255)                                        ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                      >  2:1351192/1‑119 (MQ=255)                                              aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcg                                                                                                                                      <  2:701734/81‑1 (MQ=255)                                              aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcg                                                                                                                                      >  1:701734/1‑81 (MQ=255)                                              aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTc                                                                                                                              >  2:1449885/1‑89 (MQ=255)                                              aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTc                                                                                                                              <  1:1449885/89‑1 (MQ=255)                                              aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                            >  1:338493/1‑139 (MQ=255)                                                gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                          <  2:338493/139‑1 (MQ=255)                                                   ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                       <  2:563299/139‑1 (MQ=255)                                                   ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                       <  1:505269/139‑1 (MQ=255)                                                         cctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcg                                                                                                                                      >  1:891625/1‑70 (MQ=255)                                                         cctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcg                                                                                                                                      <  2:891625/70‑1 (MQ=255)                                                           tcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCagag                                                                                       <  1:813917/115‑1 (MQ=255)                                                           tcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCagag                                                                                       >  2:813917/1‑115 (MQ=255)                                                             aTCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                           >  2:80242/1‑93 (MQ=255)                                                             aTCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                           <  1:80242/93‑1 (MQ=255)                                                                ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                          <  2:610109/139‑1 (MQ=255)                                                                       tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                           >  2:1119127/1‑83 (MQ=255)                                                                       tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                                                           <  1:1119127/83‑1 (MQ=255)                                                                       tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                   >  2:309526/1‑139 (MQ=255)                                                                             gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGTATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                             >  1:216559/1‑139 (MQ=255)                                                                              aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                            >  2:76936/1‑139 (MQ=255)                                                                              aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                            >  2:99290/1‑139 (MQ=255)                                                                                  aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                      >  2:1350412/1‑77 (MQ=255)                                                                                  aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                      <  1:1350412/77‑1 (MQ=255)                                                                                  aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATAGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                        >  1:17316/1‑139 (MQ=255)                                                                                        ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                               >  2:413337/1‑126 (MQ=255)                                                                                        ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                               <  1:413337/126‑1 (MQ=255)                                                                                        ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                  <  1:76936/139‑1 (MQ=255)                                                                                         gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt                                 <  2:864829/139‑1 (MQ=255)                                                                                          cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                          <  2:125171/97‑1 (MQ=255)                                                                                          cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                          >  1:125171/1‑97 (MQ=255)                                                                                          cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                <  2:216559/139‑1 (MQ=255)                                                                                          cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                <  2:17316/139‑1 (MQ=255)                                                                                          cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                >  1:1363678/1‑139 (MQ=255)                                                                                                               aaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGa                                                         >  2:1288822/1‑93 (MQ=255)                                                                                                               aaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGa                                                         <  1:1288822/93‑1 (MQ=255)                                                                                                                      ttGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc    <  1:1553178/139‑1 (MQ=255)                                                                                                                        gCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGACCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat  <  1:99290/139‑1 (MQ=255)                                                                                                                           |                                                                                                                                        TGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCAT  >  NC_000913/3815722‑3815979

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑