Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,569,443	A→G	pseudogene (446/921 nt)	rpnD →	truncated recombination‑promoting nuclease‑like protein RpnD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,569,443	0	A	G	100.0%	189.4 / NA	53	pseudogene (446/921 nt)	rpnD	truncated recombination‑promoting nuclease‑like protein RpnD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/24);  total (29/24)

ATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAAGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGATGGGGCTTATCGA  >  NC_000913/4569316‑4569578                                                                                                                                |                                                                                                                                        ataGAGCATGATAAACGCCAGCTGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAAcgc                                                                                                                             >  1:382899/1‑140 (MQ=255)   agagCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAAcgccg                                                                                                                           <  1:350351/140‑1 (MQ=255)     agCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCcgcg                                                                                                                         >  2:223408/1‑140 (MQ=255)         tGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTcc                                                                                                                     >  2:271984/1‑140 (MQ=255)          gATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGTTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    >  1:133964/1‑140 (MQ=255)          gATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    >  2:396579/1‑140 (MQ=255)          gATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    >  2:532950/1‑140 (MQ=255)            tAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    >  2:169508/1‑138 (MQ=255)            tAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    <  1:169508/138‑1 (MQ=255)              aaCGCCAGCCGTTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCGGTAGTCCTTACCCCTGGGCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCtg                                                                                                                <  1:223408/140‑1 (MQ=255)               aCGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCtgg                                                                                                               >  1:31947/1‑140 (MQ=255)                cGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCtggt                                                                                                              <  1:193524/140‑1 (MQ=255)                     gCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATg                                                                                                         >  1:603962/1‑140 (MQ=255)                      ccGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    <  1:610915/128‑1 (MQ=255)                      ccGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTccc                                                                                                                    >  2:610915/1‑128 (MQ=255)                      ccGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGt                                                                                                        >  2:67446/1‑140 (MQ=255)                       cGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGtt                                                                                                       <  2:358985/140‑1 (MQ=255)                         cTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTAc                                                                                                     >  2:31067/1‑140 (MQ=255)                           aCCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACt                                                                                                    >  2:443575/1‑139 (MQ=255)                           aCCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACt                                                                                                    <  1:443575/139‑1 (MQ=255)                           aCCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTg                                                                                                   <  1:244321/140‑1 (MQ=255)                                 ggTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGc                                                                                             <  1:334482/140‑1 (MQ=255)                                      tCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCa                                                                                           <  1:254664/137‑1 (MQ=255)                                      tCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCa                                                                                           >  2:254664/1‑137 (MQ=255)                                           aTGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGAcgacga                                                                                   <  1:546031/140‑1 (MQ=255)                                             gCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACgaga                                                                                 <  2:4383/140‑1 (MQ=255)                                                          ggTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGATCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCg                                                                    <  2:382899/140‑1 (MQ=255)                                                          ggTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCg                                                                    <  1:396579/140‑1 (MQ=255)                                                           gTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGc                                                                   >  2:589774/1‑140 (MQ=255)                                                              gCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCaga                                                                >  2:96829/1‑140 (MQ=255)                                                                          aCCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCAACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTg                                                    >  2:377325/1‑140 (MQ=255)                                                                                ggTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCg                                                            <  1:543294/126‑1 (MQ=255)                                                                                ggTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCg                                                            >  2:543294/1‑126 (MQ=255)                                                                                 gTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGa                                             >  1:187304/1‑140 (MQ=255)                                                                                 gTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGa                                             <  2:199749/140‑1 (MQ=255)                                                                                 gTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGa                                             >  1:199749/1‑140 (MQ=255)                                                                                 gTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGa                                             >  1:208522/1‑140 (MQ=255)                                                                                  tCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGAt                                            <  1:67446/140‑1 (MQ=255)                                                                                      tgtgCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCaa                                        >  2:371706/1‑140 (MQ=255)                                                                                      tgtgCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCaa                                        >  1:284265/1‑140 (MQ=255)                                                                                          ctggctggACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGc                                    >  2:14907/1‑140 (MQ=255)                                                                                          ctggctggACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGc                                    <  2:31947/140‑1 (MQ=255)                                                                                             gctggACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATATCGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCata                                 >  2:2246/1‑140 (MQ=255)                                                                                             gctggACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCata                                 >  2:555707/1‑140 (MQ=255)                                                                                                 gACGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCg                             <  1:371706/140‑1 (MQ=255)                                                                                                  aCGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGc                            >  1:107646/1‑140 (MQ=255)                                                                                                  aCGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGc                            <  1:271984/140‑1 (MQ=255)                                                                                                  aCGAATTTGCCGACCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGc                            >  1:95329/1‑140 (MQ=255)                                                                                                       tttGCCGCCCCGACTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGGCGAGATTGTGCAGCATCGCAGAGTCGACTTGTTGGAGTTGATCCAAAAGCATATTCGCCAgcg                       <  2:384024/140‑1 (MQ=255)                                                                                                           ccgacccgacTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTAGAGTTGATCCAAAAGCATATTCGCCAGCGCGAt                   <  1:242392/140‑1 (MQ=255)                                                                                                                ccgacTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGAt              >  1:225589/1‑140 (MQ=255)                                                                                                                ccgacTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGAt              <  2:208522/140‑1 (MQ=255)                                                                                                                ccgacTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGAt              >  2:164673/1‑140 (MQ=255)                                                                                                                    cTACCGCACGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGATgggg          <  2:187304/140‑1 (MQ=255)                                                                                                                            cGGAGGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGATGGGGCTTATCGa  <  1:555707/140‑1 (MQ=255)                                                                                                                                |                                                                                                                                        ATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGGAAGCTTTATAACGCCGCGTTCCCGCTGGTGGATGTTACTGTCGTGCCAGACGACGAGATTGTGCAGCATCGCAGAGTCGCCCTGTTGGAGTTGATCCAAAAGCATATTCGCCAGCGCGATCTGATGGGGCTTATCGA  >  NC_000913/4569316‑4569578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑