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	45 [0]	[0] 45	[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)	40 (0.950)	36/262	0.2	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

CCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGG  >  NC_000913/3815720‑3815996                                                                                                                                            |                                                                                                                                           ccTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtc                                                                                                                                        <  1:550678‑M1/143‑5 (MQ=255) ccTGCTCGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGGCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtc                                                                                                                                        <  1:543168‑M1/143‑5 (MQ=255)  cTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTCCCGAC‑AAAAAACAGGCGACTCATCAGTCGCCTTAAAAATCACTTTGCCAGCGCCGCCCTCTGCcgtcc                                                                                                                                       >  1:647539‑M1/1‑138 (MQ=255)   tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                      <  1:382153‑M1/143‑7 (MQ=255)          tAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGCCTCATCAGTCGCCTTAACAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcact                                                                                                                               >  1:16213‑M1/1‑130 (MQ=255)                         tAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAACAAGGCGCCTCATCAGTCGCCTTAAAAATAAGTTTGCCAGCGCCGCCTTCTGCcgtcccccgcacttcaatgatccgcccg                                                                                                                >  2:815967‑M1/1‑115 (MQ=255)                           aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTCTTCTACCGTC‑AGAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtc                                                                                                              <  1:692155‑M1/143‑31 (MQ=255)                            aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAACAAAAGGCGACTCATCCGTCGCCTTAAAACTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcactgcaatgatgcccccggcc                                                                                                             >  1:147472‑M1/1‑112 (MQ=255)                              tGGCGCTGATATGGATTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTATGCAAGCGCCGCCTGCTGCcgacacctgcacttcaacgaacagcctgtcttc                                                                                                           >  2:549‑M1/1‑110 (MQ=255)                                               cATGCCTTCGCTCCTCCTCTTACTTTTCTACAGACGAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttc                                                                                           <  2:620299‑M1/143‑50 (MQ=255)                                                  gCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTATGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtctccggtgctcactacattactgt                                                                                       >  2:827950‑M1/1‑90 (MQ=255)                                                     ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcgg                                                                                    >  1:458378‑M1/1‑87 (MQ=255)                                                      tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggt                                                                                   <  1:493315‑M1/143‑58 (MQ=255)                                                           cctcATCTTACTTTTCTACAGCC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtaccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctg                                                                              <  1:276512‑M1/143‑63 (MQ=255)                                                             tcATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcg                                                                            <  1:798741‑M1/143‑65 (MQ=255)                                                              cATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcgg                                                                           >  1:504407‑M1/1‑78 (MQ=255)                                                                tcgcactttTCCACAGCC‑AAAACAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTGCTGCcgtcccccgcacttcaatgatgcgcccgtcttcgggcatcactacgttcatgtcggtctctgcggca                                                                         <  1:676034‑M1/139‑68 (MQ=255)                                                                  ttACCTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAAGCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcgtcggtcatcactacgttcatgtcggtctctgcggcaga                                                                       <  1:9382‑M1/143‑70 (MQ=255)                                                                     cgttgctaccgAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtc                                                                    <  1:791839‑M1/138‑73 (MQ=255)                                                                       tttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtctt                                                                  <  1:53832‑M1/143‑75 (MQ=255)                                                                           tACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatccctccccccacgtccgtccccccgccagagtctccaac                                                              >  2:105665‑M1/1‑65 (MQ=255)                                                                                aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtatt                                                         <  1:580722‑M1/143‑84 (MQ=255)                                                                                aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatccgcccgtcttcggtcatcactacgttcatgtcagccactacgccaaagaattaaacgtatt                                                         >  1:808786‑M1/1‑60 (MQ=255)                                                                                   aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattac                                                       >  1:685463‑M1/1‑58 (MQ=255)                                                                                   aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcac                                                                                                  >  2:739271‑M1/1‑58 (MQ=255)                                                                                   aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcac                                                                                                  <  1:739271‑M1/100‑43 (MQ=255)                                                                                     aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccag                                                     >  1:313662‑M1/1‑56 (MQ=255)                                                                                     aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtctccaacgtattccag                                                     >  1:473197‑M1/1‑56 (MQ=255)                                                                                             cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaa                                             <  2:823077‑M1/143‑96 (MQ=255)                                                                                                 tcatcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttgaacggattccagaccgcaaaccgc                                         >  2:398254‑M1/1‑44 (MQ=255)                                                                                                   atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgctg                                       >  2:67352‑M1/1‑42 (MQ=255)                                                                                                    tcaggggcctgaaACATCAGTTTGCCAGCGCCGCCTTCGGCcgtccgctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttc                                      <  1:204898‑M1/137‑103 (MQ=255)                                                                                                     caGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcg                                     >  1:558724‑M1/1‑40 (MQ=255)                                                                                                           ccTTAAAAATCAGTTTGCCAGCACCGCCTTCTGCggtccccagcacggcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttc                               <  1:305526‑M1/143‑110 (MQ=255)                                                                                                                      cgtTTGCCAGCGCCGCCTTCTGCcgtcccgtgcacttcaatgacgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac                    <  2:647539‑M1/142‑121 (MQ=255)                                                                                                                      cgtTTCCCATCGCCGCCTCCTGCcgtcccctgcacctcaagtatgcgcccgtcttcggtcatcactacgctcatgtcggtctctgccgcagagtcttcaacgtactccagatcgcaaaccgcttcgccgttcacaattccgac                    <  2:76311‑M1/142‑121 (MQ=255)                                                                                                                       gTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgaca                   <  2:132006‑M1/143‑122 (MQ=255)                                                                                                                          tGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacacttccgacagaa                >  1:510283‑M1/1‑19 (MQ=255)                                                                                                                             cAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaact             >  1:601796‑M1/1‑16 (MQ=255)                                                                                                                                 gccgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcgg         <  1:199474‑M1/143‑132 (MQ=255)                                                                                                                                   cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtgggtctctccggcagagtcttcaacgtattccagatcgcaaaccgcttcgccggtcacaattccgacacaaaccgcggcc       >  2:426809‑M1/1‑10 (MQ=255)                                                                                                                                   cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacacaaactgcggct       >  2:498240‑M1/1‑10 (MQ=255)                                                                                                                                    gccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggccatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaacagcttcgccgttcaccatcccgacagcaacggcggcta      >  2:570865‑M1/1‑9 (MQ=255)                                                                                                                                     ccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgccagaaactgcggctac     >  1:826776‑M1/1‑8 (MQ=255)                                                                                                                                        tCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccat  <  1:674245‑M1/143‑139 (MQ=255)                                                                                                                                            |                                                                                                                                           CCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGG  >  NC_000913/3815720‑3815996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑