Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	Δ1 bp	pseudogene (667/669 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	3,815,880	0	C	.	100.0%	195.4 / NA	47	pseudogene (2/48 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/25);  total (22/25)

TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815749‑3816013                                                                                                                                     |                                                                                                                                      tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCggg                                                                                                                               >  2:392453/1‑139 (MQ=255)    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              >  2:421144/1‑137 (MQ=255)    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              <  1:421144/137‑1 (MQ=255)      cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCaga                                                                                                                          <  2:433735/139‑1 (MQ=255)                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGcc                                                                                                                             >  2:27651/1‑123 (MQ=255)                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGcc                                                                                                                             <  1:27651/123‑1 (MQ=255)                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAg                                                                                                            >  1:577100/1‑139 (MQ=255)                    tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGAt                                                                                                               <  2:475995/136‑1 (MQ=255)                    tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGAt                                                                                                               >  1:475995/1‑136 (MQ=255)                       cTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  1:392453/139‑1 (MQ=255)                            ctcctcATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                    <  2:229838/139‑1 (MQ=255)                                    cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCca                                                                                                                      <  2:737931/113‑1 (MQ=255)                                    cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCca                                                                                                                      >  1:737931/1‑113 (MQ=255)                                       aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                         >  2:641651/1‑139 (MQ=255)                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         >  1:291271/1‑121 (MQ=255)                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  2:291271/121‑1 (MQ=255)                                            tCTACAGACAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                     >  2:211670/1‑139 (MQ=255)                                            tCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  2:587767/118‑1 (MQ=255)                                            tCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         >  1:587767/1‑118 (MQ=255)                                              tACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGc                                                                                  >  2:675772/1‑139 (MQ=255)                                                   aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 >  1:346459/1‑103 (MQ=255)                                                   aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 <  2:346459/103‑1 (MQ=255)                                                   aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  <  1:1006462/118‑1 (MQ=255)                                                   aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  2:1006462/1‑118 (MQ=255)                                                          aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                       <  1:855412/139‑1 (MQ=255)                                                           aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcc                                                                      >  1:508484/1‑139 (MQ=255)                                                            aaGGCGACTCTTCAGTCGCCTTAAAAGTCAGATTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                     <  1:1212708/139‑1 (MQ=255)                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              <  2:140505/80‑1 (MQ=255)                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              >  1:140505/1‑80 (MQ=255)                                                                  aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCag                                                                                                                           <  2:665104/79‑1 (MQ=255)                                                                  aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCag                                                                                                                           >  1:665104/1‑79 (MQ=255)                                                                     catcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCagag                                                                                                                         <  1:532553/78‑1 (MQ=255)                                                                     catcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCagag                                                                                                                         >  2:532553/1‑78 (MQ=255)                                                                         aGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg                                                        >  1:530576/1‑139 (MQ=255)                                                                              ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 >  1:78558/1‑77 (MQ=255)                                                                              ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 <  2:78558/77‑1 (MQ=255)                                                                                     aaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                            <  2:530576/139‑1 (MQ=255)                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGt                                              <  1:111232/133‑1 (MQ=255)                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGt                                              >  2:111232/1‑133 (MQ=255)                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc                                      <  2:508484/139‑1 (MQ=255)                                                                                             tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                    <  2:615998/139‑1 (MQ=255)                                                                                              gCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  1:832044/1‑76 (MQ=255)                                                                                              gCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  <  2:832044/76‑1 (MQ=255)                                                                                                cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                 <  1:641651/139‑1 (MQ=255)                                                                                                cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                 <  2:967941/139‑1 (MQ=255)                                                                                                     ccgccTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                            <  2:497213/139‑1 (MQ=255)                                                                                                                         aTGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa        >  2:449698/1‑139 (MQ=255)                                                                                                                            gattcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATCTCGGTCTCTGCGGCagag     <  1:675772/139‑1 (MQ=255)                                                                                                                              ttcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  2:783251/1‑44 (MQ=255)                                                                                                                              ttcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCCTCa                                                                                                  <  1:783251/44‑1 (MQ=255)                                                                                                                               tcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt  >  2:678157/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                      TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815749‑3816013

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: ‑