Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3815859	3815940	82	56 [0]	[0] 57	[rph]–[rph]	[rph],[rph]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3815858	0 (0.000)	53 (0.880)	45/264	0.3	100%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913	3815941 =	0 (0.000)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTT  >  NC_000913/3815801‑3816083                                                                                                                                             |                                                                                                                                               acctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcaatttgccagcgccaccttatgcCGt                                                                                                                                              >  2:607984‑M2/141‑143 (MQ=255)  cctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgttcctcatcttaattttatagtgtgaaaaaaaaggcgactcatcagtcgccttaaaaatccgtttgccagcgccgccttccgcCGTc                                                                                                                                             >  1:542012‑M2/140‑143 (MQ=255)   ctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTcc                                                                                                                                            >  1:1041627‑M2/139‑143 (MQ=255)    tgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaacggcgactcatcagtcgccttaagaatcagtttgccagcgccgccctctgcCGTtcc                                                                                                                                           >  2:809029‑M2/138‑143 (MQ=255)    tgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaactcagtttgccagcgccgccttctgcCGTccc                                                                                                                                           <  2:143476‑M2/6‑1 (MQ=255)    tgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgacagcgccgccttctgcCGTccc                                                                                                                                           >  2:613748‑M2/138‑143 (MQ=255)         gctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgacgcatcngtcgccttaaaaatcagtttgcccgccccgcctgctccAGTCGCCTGCa                                                                                                                                      >  1:825035‑M2/133‑143 (MQ=255)               cgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCaa                                                                                                                                <  2:660592‑M2/17‑1 (MQ=255)                gcaaagtcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAat                                                                                                                               <  1:383290‑M2/18‑1 (MQ=255)                   aattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttactgttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAatgat                                                                                                                            <  1:497217‑M2/21‑1 (MQ=255)                    attcaatcaaccggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgctgccttctgcCGTCCCCTGCACTTCAatgatg                                                                                                                           <  2:505202‑M2/22‑1 (MQ=255)                     ttcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATgc                                                                                                                          >  1:860901‑M2/121‑143 (MQ=255)                         gtgagctggcgttgatgtggtttcatgccttcgctcctcatcttacttttgtgcagaaaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGccc                                                                                                                      <  1:1111748‑M2/27‑1 (MQ=255)                          taaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCg                                                                                                                     <  2:392144‑M2/28‑1 (MQ=255)                              ctggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATCATGCGCCCGGCtt                                                                                                                 >  2:388045‑M2/112‑143 (MQ=255)                               tggcgctcatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTc                                                                                                                <  2:277462‑M2/33‑1 (MQ=255)                                 gcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                                                                                              <  2:1041627‑M2/35‑1 (MQ=255)                                  cgcttatgtggtttcatgccgtcgctcctcatcttacctttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                                                                                             <  2:1163600‑M2/36‑1 (MQ=255)                                     tgattgggttccatgccttcgctccgcatcttactgtcctacggacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgcctcctgcCGTCCCCTGCACGTCAATGATGCGCCCGTCTTCGGtcat                                                                                                          <  2:490954‑M2/39‑1 (MQ=255)                                        tatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                                                                                       <  1:94073‑M2/42‑1 (MQ=255)                                          tggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATAATTCGCCCGTCTTCCATAATCActc                                                                                                     >  2:144635‑M2/100‑142 (MQ=255)                                                  tgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATg                                                                                             >  2:162503‑M2/92‑143 (MQ=255)                                                    ccttcgctcctctttttactttgcttgatacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTc                                                                                           <  1:321095‑M2/54‑1 (MQ=255)                                                                  cttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag                                                                             >  1:54928‑M2/76‑143 (MQ=255)                                                                   ttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagttcgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                                            <  1:401161‑M2/69‑1 (MQ=255)                                                                   ttacttgtcgacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGGCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                                            <  1:504358‑M2/69‑1 (MQ=255)                                                                   ttactgttctacagacacaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgcagccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                                            <  2:562071‑M2/69‑1 (MQ=255)                                                                    tacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACCACGCTCATGTCCGTCTCCGCGGCcgag                                                                           >  2:648705‑M2/74‑143 (MQ=255)                                                                           ctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCaa                                                                    <  1:709929‑M2/77‑1 (MQ=255)                                                                            tacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCATTGTTGTGCCCGTCTTCGGTTATCACTACGTTCATGTCGGTCTCTGCTGCAGAGTCTGCAAc                                                                   >  1:160210‑M2/66‑143 (MQ=255)                                                                            tacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTACGACAGAGACTTcaaa                                                                   >  1:740087‑M2/66‑142 (MQ=255)                                                                               agacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCGTGCCGGTCTCTGCGGCAGAGTCTTCAccgga                                                                >  1:357080‑M2/63‑141 (MQ=255)                                                                                gacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCACCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAt                                                               <  1:681317‑M2/82‑1 (MQ=255)                                                                                      gtgcgggcgacccaccagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCATTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGa                                                         <  2:860901‑M2/88‑1 (MQ=255)                                                                                       aaaaggcgactcatcagtccccttaaaaatcagtttgcgagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                        <  1:964444‑M2/89‑1 (MQ=255)                                                                                       aaaaggccactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGGTGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                        <  2:464433‑M2/89‑1 (MQ=255)                                                                                           ggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCa                                                    <  1:226039‑M2/93‑1 (MQ=255)                                                                                              gactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCCACGTATTCCAGgtcgctcac                                                 >  1:402535‑M2/48‑139 (MQ=255)                                                                                              gactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAAc                                                 <  1:964043‑M2/96‑1 (MQ=255)                                                                                              gactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAGCGCAAAc                                                 >  1:1158451‑M2/48‑143 (MQ=255)                                                                                                ctcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCg                                               >  2:535190‑M2/46‑143 (MQ=255)                                                                                                   atcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAACCCGCtt                                            >  1:546537‑M2/43‑143 (MQ=255)                                                                                                   atcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCtt                                            >  1:1074012‑M2/43‑143 (MQ=255)                                                                                                    tcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCGATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTc                                           <  1:580275‑M2/102‑1 (MQ=255)                                                                                                        tcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCCTCACTACGTTCATGTCGGGCTCGGCGGCAGAGTCTTCAACGTATTCCAGCTCGCGaaccgctcacacg                                       >  2:132557‑M2/38‑137 (MQ=255)                                                                                                             ttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGGGGAAAAGTCGCCAACGTCTTCGATATCGCAGACCGCTTCGCCGTTcac                                  >  1:1150172‑M2/33‑143 (MQ=255)                                                                                                                      agtttgccagcgccgccttctgcAGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGAc                         <  2:1065848‑M2/120‑1 (MQ=255)                                                                                                                        tttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCGACGTATTCAAGATCGCAAAACGCTGCGCCGTTCACGATTCCGagag                       >  1:294037‑M2/22‑143 (MQ=255)                                                                                                                          tgccagcgccgcctgcggcCGTCCCCTGCGCTTCAATCATTCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGaa                     <  1:1095792‑M2/124‑1 (MQ=255)                                                                                                                           gccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGaaa                    <  1:398375‑M2/125‑1 (MQ=255)                                                                                                                              agcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGAc                         >  1:52740‑M2/16‑135 (MQ=255)                                                                                                                              agcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGAc                         <  2:52740‑M2/120‑1 (MQ=255)                                                                                                                                cgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTCCACAATTCCGCCGGAAACTCCg               >  1:718597‑M2/14‑143 (MQ=255)                                                                                                                                      cttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAGCCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTAcc         <  2:157891‑M2/136‑1 (MQ=255)                                                                                                                                        tctgcCGTCCCCTGCACTTCACTGACGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGCCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCAt       <  1:994624‑M2/138‑1 (MQ=255)                                                                                                                                           gcCGTCCCCTGCACTTCAATGATGGGCCCTTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATccc    <  2:196148‑M2/141‑1 (MQ=255)                                                                                                                                             cGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCtt  <  1:613748/143‑1 (MQ=255)                                                                                                                                             |                                                                                                                                               AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTT  >  NC_000913/3815801‑3816083

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑