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	55 [0]	[2] 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)	51 (0.970)	45/264	0.1	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

ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCC  >  NC_000913/3815799‑3816080                                                                                                                                               |                                                                                                                                              acacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcc                                                                                                                                               <  2:151065‑M2/1‑1 (MQ=255) acacctgctcgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcc                                                                                                                                               <  2:786690‑M2/1‑1 (MQ=255)  cacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCg                                                                                                                                              >  1:306966‑M2/142‑143 (MQ=255)       gcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaataagtttgccagcgccgcctactgcCGTcccc                                                                                                                                         >  2:95882‑M2/137‑143 (MQ=255)         gtgctaagcgcaaatccaataacctggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTg                                                                                                                                       <  1:597497‑M2/9‑1 (MQ=255)                 cgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCaa                                                                                                                             >  1:25833‑M2/127‑143 (MQ=255)                 cgcaaatgcaatganctggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCaa                                                                                                                             <  1:832988‑M2/17‑1 (MQ=255)                     aattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAatgat                                                                                                                         >  2:512338‑M2/123‑143 (MQ=255)                          aataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGcc                                                                                                                    <  1:745129‑M2/26‑1 (MQ=255)                           ataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaacaaaaagacgactcatcagccgccttaaaaatcagtttgccagcgccgcattctgcCGTCCCCCGACAC‑‑TCAATGCTGGGccc                                                                                                                   >  2:337068‑M2/117‑143 (MQ=255)                             aaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaacaaaaaggcgactcatcagtcgccttaaaaatcagtttgcccgcgccgcgttctgcCGTCCCTCG‑CAC‑TTCAACGATGcgccccc                                                                                                                 >  2:72920‑M2/115‑141 (MQ=255)                             aaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagagcagacgtcagcCGTCCCCTG‑CAC‑TTCACTGCTGCGCCCGt                                                                                                                 >  1:686683‑M2/115‑143 (MQ=255)                              aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcataagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCCATGCTGCGCccgcc                                                                                                                >  2:499731‑M2/114‑141 (MQ=255)                               actggcgctgatatggtttcatgccttcgctcctcatcttactttactacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCcgtgt                                                                                                               >  1:192156‑M2/113‑141 (MQ=255)                                  ggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCg                                                                                                            <  1:156873‑M2/34‑1 (MQ=255)                                   gcgctgctatcgtctcatgccttcgctcctcaccttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagttcgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCgg                                                                                                           <  2:69376‑M2/35‑1 (MQ=255)                                   gcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaacaaggcgactcatcagtcgccttaaaaatcagtttgccaacgccgcctgctccCGCCCCCTG‑CAC‑ATCACTCATGCGCCCGCCTCCgg                                                                                                           >  2:587275‑M2/109‑143 (MQ=255)                                     gctgatatggttgcatgcctccgctcctcgtcttactttcctacagacagaagaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGtc                                                                                                         <  2:594364‑M2/37‑1 (MQ=255)                                       tgagatggtttcatgccgtcgctcctcatcttacttgtctacagacaaaaaaaaggcgactcaccagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGtcat                                                                                                       <  2:70251‑M2/39‑1 (MQ=255)                                             ggtttcatgccttcgctcctcatcttacttttctacagacaaaaacaaggcgactcatcagtcgccttaaacatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGCCTTCGGTCATCactcc                                                                                                 >  2:846217‑M2/99‑141 (MQ=255)                                                ttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                                                                                              >  1:804854‑M2/96‑143 (MQ=255)                                                 tcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                                                                                             >  1:601582‑M2/95‑143 (MQ=255)                                                 ccacgccttcgctcctcatcttacttgcctaccgacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGAGGCGCCCGTCTTCGGTCATCACTACGTTc                                                                                             <  1:116153‑M2/49‑1 (MQ=255)                                                   atgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCCCTACGgtcct                                                                                           >  1:860790‑M2/93‑141 (MQ=255)                                                    tgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATg                                                                                          >  1:306600‑M2/92‑143 (MQ=255)                                                          cgcttctcatctgactcttctaccgacaacaaaaaggcgactcatcagtcgccttaaaaatcattttgtcagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtc                                                                                    <  2:991278‑M2/58‑1 (MQ=255)                                                           gctcctcatcttacttgtctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct                                                                                   <  1:335697‑M2/59‑1 (MQ=255)                                                               ctcaccttacctttctacccacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGc                                                                               <  1:351721‑M2/63‑1 (MQ=255)                                                                         ttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt                                                                     >  1:155134‑M2/71‑143 (MQ=255)                                                                              tacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGCGGCTTCAAc                                                                >  1:381336‑M2/66‑143 (MQ=255)                                                                               acagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGGCGAGTCTTCAACg                                                               >  2:512784‑M2/65‑143 (MQ=255)                                                                                   acaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCCACGGAtt                                                           >  1:621690‑M2/61‑143 (MQ=255)                                                                                    caaaagaaaggcgcgtcttcggtctccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCGTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                          <  2:45038‑M2/84‑1 (MQ=255)                                                                                    caaaaaaaaggcgactcatcagtcgccttaaaaatcagttcgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                          <  1:4672‑M2/84‑1 (MQ=255)                                                                                     aaaaaaaaggcgactcatcagtcgcattaaatatcagttttccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTcc                                                         <  1:956373‑M2/85‑1 (MQ=255)                                                                                      aaaaaaaggcgtctcagcggtcgccttaaaaatcagtttgccagcgccgccttcggcCGTCCCCTG‑CAC‑TTCCATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCATCgtatttta                                                        <  2:175240‑M2/86‑4 (MQ=255)                                                                                      aaaaaaaggcgactcagcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCa                                                        <  1:607243‑M2/86‑1 (MQ=255)                                                                                       aaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCGTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAGTGCAg                                                       >  1:560419‑M2/57‑143 (MQ=255)                                                                                        ataaaggcgactcatcagtcgcctcaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGa                                                      <  1:566725‑M2/88‑1 (MQ=255)                                                                                        aaaaaggcgactcatcagtcgcttgaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGCTGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGa                                                      <  2:428142‑M2/88‑1 (MQ=255)                                                                                               cgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCaaa                                               <  1:390911‑M2/95‑1 (MQ=255)                                                                                                      tcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATAATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTc                                        >  1:663911‑M2/42‑143 (MQ=255)                                                                                                            gccttaaaaatcggtgcgccagcgccgccttctccCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGtt                                  <  2:80588‑M2/108‑1 (MQ=255)                                                                                                              cttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCCTCGCCGTTca                                >  2:227276‑M2/34‑143 (MQ=255)                                                                                                              cttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCAGTCATCACTACGCTCATGTCGGTCTCTGCGGCACAGCCTTCACCGTATTCCACCTCGCACACCCCACCGCCCTTca                                >  2:586448‑M2/34‑143 (MQ=255)                                                                                                                   aaagcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCCGAGCCTTCCACGTATTCCAGATCGCAAACCGCTTCGCCGTCCACACtt                           >  2:677874‑M2/29‑143 (MQ=255)                                                                                                                    aatcagtttgccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTCTTCCAGATCGCAAACCGCTTCGCCGTTCACAattg                          >  1:352576‑M2/28‑142 (MQ=255)                                                                                                                       catgtcgccagcgccgcctactgcCGTCCCCTG‑CAC‑ATCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCAGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGa                       <  2:544710‑M2/119‑1 (MQ=255)                                                                                                                              ccagcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGCCAGAAAc                >  1:254811‑M2/18‑143 (MQ=255)                                                                                                                                agcgccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACCGAAACTg              >  1:647377‑M2/16‑143 (MQ=255)                                                                                                                                   gccGCCTTCTGCCGTCCTCTC‑CAC‑CTGATGGTTGCGCCCGTGCTCGGTTATCGTTGCGTTCGTGTTGTTGTCTGCGTATGAGTCTTCAGCTTATGCCGGGTCGCAAACCGCGTGGCCGTTGACAATTCCGACAGAAACTGCgg           <  2:939515/141‑1 (MQ=255)                                                                                                                                    ccgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACTTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGc          <  1:95882‑M2/132‑1 (MQ=255)                                                                                                                                     cgccttctgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACAGCGGCt         >  2:810591‑M2/11‑143 (MQ=255)                                                                                                                                        cTTCTGCCGTCCCCTG‑CAC‑TTCATTGATGCGCCCGTCTTCGGTCATCCCTACGTTCATGTCGAACTCTGCCGCAGAGTCTTCCACGTATTGCAGATCAAAAACCGCTTCGCCGTCTACAACTCCGACGTCAACTCCGGATAcc      >  2:1006195/1‑143 (MQ=255)                                                                                                                                            tgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATcc  <  1:512338‑M2/140‑1 (MQ=255)                                                                                                                                            tgcCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATcc  <  1:803530‑M2/140‑1 (MQ=255)                                                                                                                                            tgcCGTCCCC‑G‑TACATTCAATGCTGCGCCTGTCTACGGGCATCACTACGTTCTTGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATcc  <  2:294932‑M2/140‑1 (MQ=255)                                                                                                                                               |                                                                                                                                              ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTG‑CAC‑TTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCC  >  NC_000913/3815799‑3816080

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: ‑