Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,863	C→T	pseudogene (19/48 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	3,815,863	0	C	T	100.0%	161.9 / NA	50	pseudogene (19/48 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/25);  total (25/25)

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGG  >  NC_000913/3815741‑3815996                                                                                                                           |                                                                                                                                        cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                         <  1:1489780/139‑1 (MQ=255)   aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑cc                                                                                                                     >  1:988213/1‑139 (MQ=255)           gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGc                                                                                                             <  2:238448/139‑1 (MQ=255)             gcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCa                                                                                                           <  2:1649243/139‑1 (MQ=255)                 atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  >  1:11410/1‑128 (MQ=255)                 atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  <  2:11410/128‑1 (MQ=255)                        ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCACCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAg                                                                                                <  1:856398/139‑1 (MQ=255)                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCa                                                                                                           <  2:996204/125‑1 (MQ=255)                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCa                                                                                                           >  1:996204/1‑125 (MQ=255)                                 tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATgg                                                                                                                                 >  1:206950/1‑99 (MQ=255)                                 tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATgg                                                                                                                                 <  2:206950/99‑1 (MQ=255)                                         cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTctgg                                                                               <  2:988213/139‑4 (MQ=255)                                                 ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                        >  1:236751/1‑122 (MQ=255)                                                 ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                        <  2:236751/122‑1 (MQ=255)                                                 ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTg                                                                           >  2:1349485/1‑134 (MQ=255)                                                 ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTg                                                                           <  1:1349485/134‑1 (MQ=255)                                                    tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGc                                                                     >  2:1294925/1‑139 (MQ=255)                                                      tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGc                                                                 >  2:977323/1‑139 (MQ=255)                                                         aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGTGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                        >  2:618609/1‑114 (MQ=255)                                                         aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGTGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                        <  1:618609/114‑1 (MQ=255)                                                             aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  <  1:1518165/84‑1 (MQ=255)                                                             aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  >  2:1518165/1‑84 (MQ=255)                                                             aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGc                                                          >  2:448736/1‑139 (MQ=255)                                                                      gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                 <  1:448736/139‑1 (MQ=255)                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  <  1:1652787/74‑1 (MQ=255)                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCt                                                                                                                  >  2:1652787/1‑74 (MQ=255)                                                                         aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                 >  1:1507430/1‑136 (MQ=255)                                                                         aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                 <  2:1507430/136‑1 (MQ=255)                                                                         aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCAc                                              >  1:43908/1‑139 (MQ=255)                                                                                    gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                   >  1:1331955/1‑139 (MQ=255)                                                                                     ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                  >  2:923962/1‑139 (MQ=255)                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTg                                                           >  2:1161407/1‑112 (MQ=255)                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTg                                                           <  1:1161407/112‑1 (MQ=255)                                                                                        tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTa                                                                                         <  1:289206/82‑1 (MQ=255)                                                                                        tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTa                                                                                         >  2:289206/1‑82 (MQ=255)                                                                                                   ttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                    <  2:1331955/139‑1 (MQ=255)                                                                                                   ttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                    <  2:43908/139‑1 (MQ=255)                                                                                                    tGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                         >  2:891245/1‑40 (MQ=255)                                                                                                    tGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                         <  1:891245/40‑1 (MQ=255)                                                                                                    tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                   >  1:602551/1‑139 (MQ=255)                                                                                                        aGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt               <  2:452632/139‑1 (MQ=255)                                                                                                          cgccgcCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                >  2:314162/1‑120 (MQ=255)                                                                                                          cgccgcCTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                <  1:314162/120‑1 (MQ=255)                                                                                                            ccgccTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                        <  2:1030692/63‑1 (MQ=255)                                                                                                            ccgccTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGCCCAGAGCCAACAAGATGAGTAg                                                                                        >  1:1030692/1‑63 (MQ=255)                                                                                                               ccTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCa        >  2:846107/1‑139 (MQ=255)                                                                                                                cTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTc                                                                                  <  2:216927/65‑1 (MQ=255)                                                                                                                cTTCTGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTc                                                                                  >  1:216927/1‑65 (MQ=255)                                                                                                                    tGCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg   <  1:977323/139‑1 (MQ=255)                                                                                                                     gCGTCGTTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTC‑TGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCgg  >  1:674986/1‑139 (MQ=255)                                                                                                                           |                                                                                                                                        CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGG  >  NC_000913/3815741‑3815996

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: ‑