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	39 [0]	[0] 39	[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)	37 (1.010)	31/264	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

CACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTC  >  NC_000913/3815718‑3815998                                                                                                                                             |                                                                                                                                             cacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcg                                                                                                                                            <  2:415956‑M1/143‑3 (MQ=255) cacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcc                                                                                                                                            >  1:540551‑M1/1‑141 (MQ=255) cacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgt                                                                                                                                           >  1:542571‑M1/1‑140 (MQ=255)    cTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGAGATGGTTTCATGCCTTCGCTCCTCCTCTTACGTTTCTACAGACAAAAAAAAGGCGCCTCATCAGTCGCCGTAAAAATCAGTTTGCGAGGCCCGCCTTCTGCcctcc                                                                                                                                         >  1:285223‑M1/1‑138 (MQ=255)       cgagctaagCGCAAATTCAATAAACTGACGCTGATATGGTTTCATGCATTCGCTCCTCATCTTACTTTTCTACAGAC‑‑AAAAAAGACGACTCATCAGTCACCTTAAAAATCAGTTTGCCAGCGCCGCCTCCAGCcgccccctgc                                                                                                                                    >  2:478064‑M1/4‑133 (MQ=255)        ttgctAAGCGCAAATTCAATAAACTGGCGCTGATAGGGGCTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctg                                                                                                                                     <  1:298216‑M1/143‑10 (MQ=255)                cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                                             <  1:253347‑M1/143‑18 (MQ=255)                  cAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCGTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatg                                                                                                                           <  2:167848‑M1/143‑20 (MQ=255)                          aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgccc                                                                                                                   >  2:524469‑M1/1‑116 (MQ=255)                                gggcGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACGTTTCTACAGGCAAAAAAAAGGCGACGCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtaccctgcacttcaatgatgcgcccgtcttc                                                                                                             <  2:701958‑M1/142‑34 (MQ=255)                                   cgcTTAGATGGTTGCATGCCTTCTCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGGCGCCTTAAAAATCAGTCTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggt                                                                                                          <  2:230452‑M1/143‑37 (MQ=255)                                      tcatatggTTTCATGCCTCCCCCCCGCATCTCACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcat                                                                                                       <  1:187189‑M1/141‑40 (MQ=255)                                      cgaTATGGTGTCATGCCTTCGCACCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcat                                                                                                       <  1:112812‑M1/142‑40 (MQ=255)                                          atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttccatgatgcgcccgtcttcggtcatcact                                                                                                   >  1:713762‑M1/1‑100 (MQ=255)                                           tGGTTTCATGCCTTCGCGCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcacta                                                                                                  <  1:388453‑M1/143‑45 (MQ=255)                                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAACAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccctcttcggtcctccctccgttcat                                                                                           >  1:124412‑M1/1‑92 (MQ=255)                                                    gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcattgatgcgcccgccttcggtcgtcactacttgcatgt                                                                                         >  1:657740‑M1/1‑90 (MQ=255)                                                     ccgtcgcTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGGCAGCGCCGCCTTCTGTcgtcccctgcacttgaatgatgcgcccgtcttcggtcatcactacgttcatgtc                                                                                        <  2:15567‑M1/140‑55 (MQ=255)                                                       ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactccgttcatgtcgg                                                                                      >  1:548784‑M1/1‑87 (MQ=255)                                                                  ttttacTTTTCTACAGATAAAAAAGAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCGTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcgttcatcactacgctcatgtcggtctctgcggca                                                                           <  2:373873‑M1/141‑68 (MQ=255)                                                                    ttgctttTCTACAGACAAACAATAGGCGACTCATCAGTCGCCTTAAACATCATTTTGCCAGCGCCGCCCTCTGAcgtcctctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                         <  2:9349‑M1/140‑70 (MQ=255)                                                                    ctaCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTGCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcacttcgttcatgtcggtctctgcggcaga                                                                         <  1:217943‑M1/142‑70 (MQ=255)                                                                                  aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagccttcaacgtatg                                                           >  2:544948‑M1/1‑60 (MQ=255)                                                                                     aaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctcttcggcagagtcttcatcgtattcaa                                                        >  1:54086‑M1/1‑57 (MQ=255)                                                                                       aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactccgttcctgtcggtccctgcggcagactcttcaacgtattacacc                                                      >  2:53394‑M1/1‑55 (MQ=255)                                                                                        aaaaGGCTGCTCATCAGTCGCCTTAAGAATCAGTTTTCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                     <  2:506327‑M1/143‑90 (MQ=255)                                                                                        aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                     <  1:587057‑M1/143‑90 (MQ=255)                                                                                                        gTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcagcagagtcttcaacgtattccagatcgcaaaccgcttcgcc                                     <  2:709893‑M1/143‑106 (MQ=255)                                                                                                              ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattcaagatcgcaaaccgcttcgccgttcac                               >  1:460897‑M1/1‑32 (MQ=255)                                                                                                              tcaaaaatcAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcac                               <  1:471471‑M1/141‑112 (MQ=255)                                                                                                                aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacca                             >  1:468454‑M1/1‑30 (MQ=255)                                                                                                                aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaa                             <  1:524469‑M1/143‑114 (MQ=255)                                                                                                                  aaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctacactccaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaatt                           <  1:363537‑M1/143‑116 (MQ=255)                                                                                                                   aaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacacttc                          >  2:199370‑M1/1‑27 (MQ=255)                                                                                                                    aTCAGTTTGCCAGCGCCGCCTTCTGCcgtcctcaacaactgatggaagcgcccgtcttcggtcatcactacgttcatgtcgctctctgcgccagaggcttcaacgtattctagatcgcaaaccgcttcgccgttcaccattcc                         >  2:624989‑M1/1‑26 (MQ=255)                                                                                                                    aTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcctcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccaaatggcaaaccgcttcgacgttcacaattcc                         >  1:656356‑M1/1‑26 (MQ=255)                                                                                                                          ttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacaga                   >  1:395152‑M1/1‑20 (MQ=255)                                                                                                                                    cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattcaagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggct         >  2:399046‑M1/1‑10 (MQ=255)                                                                                                                                           tGCcgtcccctgcatgtcgttgatgcgcccgtcttcggtcatcactacgttcctgtcggtctctgcggcagagtcttcaacgtattccagttcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatcc  <  2:549487‑M1/143‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             CACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTC  >  NC_000913/3815718‑3815998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑