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

ACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCT  >  NC_000913/3815719‑3815999                                                                                                                                            |                                                                                                                                              acCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAATTTGCCAGCGCCACCTTATGCcgt                                                                                                                                            >  2:607984‑M1/1‑140 (MQ=255)  ccTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGTTCCTCATCTTAATTTTATAGTGTGAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCCGTTTGCCAGCGCCGCCTTCCGCcgtc                                                                                                                                           >  1:542012‑M1/1‑139 (MQ=255)   cTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcc                                                                                                                                          >  1:1041627‑M1/1‑138 (MQ=255)    tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAACGGCGACTCATCAGTCGCCTTAAGAATCAGTTTGCCAGCGCCGCCCTCTGCcgttcc                                                                                                                                         >  2:809029‑M1/1‑137 (MQ=255)    tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAACTCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                         <  2:143476‑M1/143‑7 (MQ=255)    tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGACAGCGCCGCCTTCTGCcgtccc                                                                                                                                         >  2:613748‑M1/1‑137 (MQ=255)         gctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACGCATCNGTCGCCTTAAAAATCAGTTTGCCCGCCCCGCCTGCTCCagtcgcctgca                                                                                                                                    >  1:825035‑M1/1‑132 (MQ=255)               cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                                              <  2:660592‑M1/143‑18 (MQ=255)                gcAAAGTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                             <  1:383290‑M1/143‑19 (MQ=255)                   aaTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTGTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgat                                                                                                                          <  1:497217‑M1/143‑22 (MQ=255)                    aTTCAATCAACCGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCTGCCTTCTGCcgtcccctgcacttcaatgatg                                                                                                                         <  2:505202‑M1/143‑23 (MQ=255)                     ttCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgc                                                                                                                        >  1:860901‑M1/1‑120 (MQ=255)                         gtgagctggcgTTGATGTGGTTTCATGCCTTCGCTCCTCATCTTACTTTTGTGCAGAAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgccc                                                                                                                    <  1:1111748‑M1/138‑28 (MQ=255)                          tAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccg                                                                                                                   <  2:392144‑M1/143‑29 (MQ=255)                              cTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatcatgcgcccggctt                                                                                                               >  2:388045‑M1/1‑111 (MQ=255)                               tGGCGCTCATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttc                                                                                                              <  2:277462‑M1/143‑34 (MQ=255)                                 gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcgg                                                                                                            <  2:1041627‑M1/143‑36 (MQ=255)                                  cgcTTATGTGGTTTCATGCCGTCGCTCCTCATCTTACCTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggt                                                                                                           <  2:1163600‑M1/143‑37 (MQ=255)                                     tgattgggttccatGCCTTCGCTCCGCATCTTACTGTCCTACGGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTCCTGCcgtcccctgcacgtcaatgatgcgcccgtcttcggtcat                                                                                                        <  2:490954‑M1/137‑40 (MQ=255)                                        tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcac                                                                                                     <  1:94073‑M1/143‑43 (MQ=255)                                          tGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaataattcgcccgtcttccataatcactc                                                                                                   >  2:144635‑M1/1‑99 (MQ=255)                                                  tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatg                                                                                           >  2:162503‑M1/1‑91 (MQ=255)                                                    ccTTCGCTCCTCTTTTTACTTTGCTTGATACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtc                                                                                         <  1:321095‑M1/143‑55 (MQ=255)                                                                  cTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcag                                                                           >  1:54928‑M1/1‑75 (MQ=255)                                                                   ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTCGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                          <  1:401161‑M1/143‑70 (MQ=255)                                                                   ttACTTGTCGACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccggcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                          <  1:504358‑M1/143‑70 (MQ=255)                                                                   ttACTGTTCTACAGACACAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCAGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                          <  2:562071‑M1/143‑70 (MQ=255)                                                                    tACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcaccacgctcatgtccgtctccgcggccgag                                                                         >  2:648705‑M1/1‑73 (MQ=255)                                                                           cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                                                  <  1:709929‑M1/143‑78 (MQ=255)                                                                            tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcattgttgtgcccgtcttcggttatcactacgttcatgtcggtctctgctgcagagtctgcaac                                                                 >  1:160210‑M1/1‑65 (MQ=255)                                                                            tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctacgacagagacttcaaa                                                                 >  1:740087‑M1/1‑65 (MQ=255)                                                                               aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcgtgccggtctctgcggcagagtcttcaccgga                                                              >  1:357080‑M1/1‑62 (MQ=255)                                                                                gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcacccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtat                                                             <  1:681317‑M1/143‑83 (MQ=255)                                                                                      gtgcgggcgaccCACCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcattacgttcatgtcggtctctgcggcagagtcttcaacgtattccaga                                                       <  2:860901‑M1/138‑89 (MQ=255)                                                                                       aaaaGGCGACTCATCAGTCCCCTTAAAAATCAGTTTGCGAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                      <  1:964444‑M1/143‑90 (MQ=255)                                                                                       aaaaGGCCACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatggtgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                      <  2:464433‑M1/143‑90 (MQ=255)                                                                                           ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgca                                                  <  1:226039‑M1/143‑94 (MQ=255)                                                                                              gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttccacgtattccaggtcgctcac                                               >  1:402535‑M1/1‑47 (MQ=255)                                                                                              gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaac                                               <  1:964043‑M1/143‑97 (MQ=255)                                                                                              gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagagcgcaaac                                               >  1:1158451‑M1/1‑47 (MQ=255)                                                                                                cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccg                                             >  2:535190‑M1/1‑45 (MQ=255)                                                                                                   atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaacccgctt                                          >  1:546537‑M1/1‑42 (MQ=255)                                                                                                   atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgctt                                          >  1:1074012‑M1/1‑42 (MQ=255)                                                                                                    tcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcgatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttc                                         <  1:580275‑M1/143‑103 (MQ=255)                                                                                                        tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcctcactacgttcatgtcgggctcggcggcagagtcttcaacgtattccagctcgcgaaccgctcacacg                                     >  2:132557‑M1/1‑37 (MQ=255)                                                                                                             ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctggggaaaagtcgccaacgtcttcgatatcgcagaccgcttcgccgttcac                                >  1:1150172‑M1/1‑32 (MQ=255)                                                                                                                      aGTTTGCCAGCGCCGCCTTCTGCagtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac                       <  2:1065848‑M1/143‑121 (MQ=255)                                                                                                                        tttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcgacgtattcaagatcgcaaaacgctgcgccgttcacgattccgagag                     >  1:294037‑M1/1‑21 (MQ=255)                                                                                                                          tGCCAGCGCCGCCTGCGGCcgtcccctgcgcttcaatcattcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaa                   <  1:1095792‑M1/143‑125 (MQ=255)                                                                                                                           gCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaa                  <  1:398375‑M1/143‑126 (MQ=255)                                                                                                                              aGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac                       >  1:52740‑M1/1‑15 (MQ=255)                                                                                                                              aGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac                       <  2:52740‑M1/135‑121 (MQ=255)                                                                                                                                cgccgcCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgtccacaattccgccggaaactccg             >  1:718597‑M1/1‑13 (MQ=255)                                                                                                                                      cTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaagccgcttcgccgttcacaattccgacagaaactgcggctacc       <  2:157891‑M1/143‑137 (MQ=255)                                                                                                                                        tCTGCcgtcccctgcacttcactgacgcgcccgtcttcggtcatcactacgttcatgtcggcctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccat     <  1:994624‑M1/143‑139 (MQ=255)                                                                                                                                           gCcgtcccctgcacttcaatgatgggcccttcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatccc  <  2:196148‑M1/143‑142 (MQ=255)                                                                                                                                            |                                                                                                                                              ACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCT  >  NC_000913/3815719‑3815999

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: ‑