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	46 [0]	[0] 46	[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)	46 (1.000)	39/264	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

CACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATC  >  NC_000913/3815718‑3815980                                                                                                                                             |                                                                                                                           cacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGCCCCCCCCCTCTCCTTAAGGGTCAGTTAGCCAGCGCCGCCTTCTGCcg                                                                                                                          >  1:413238‑M1/1‑141 (MQ=255) cacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcg                                                                                                                          >  1:724253‑M1/1‑141 (MQ=255)     tacgtgctaagcGCAACTTCGATCAACTGGCGCTGATATGATTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                      <  2:235602‑M1/139‑7 (MQ=255)            tAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcact                                                                                                               >  1:846809‑M1/1‑130 (MQ=255)              aGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACCAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATAAGTTTGCCAGCGACGCCTTCTGCcgtcccctgcacttc                                                                                                             >  1:483462‑M1/1‑128 (MQ=255)                    aaTTCAATAAACTCGCGCTGATATGGTTTCATGCCTTCGCACCTCATCTTACTATTCTACCCACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAACCAGTCTGCCAGCGCCGCCTTCTGCcgccccccgcacttcaatgat                                                                                                       <  2:214188‑M1/143‑22 (MQ=255)                     aTTCAATAAACTCGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatg                                                                                                      <  1:477110‑M1/143‑23 (MQ=255)                          aTAAACTGGCGCTGATATGGTTTCATGCCGTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgccc                                                                                                 <  1:447629‑M1/143‑28 (MQ=255)                                     cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGCCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccccggcacatcaatcatgcgcccgccctcggtca                                                                                      >  2:220021‑M1/1‑105 (MQ=255)                                      gaatatggTTGCGATCCTTCGCTCCCCATCTTACTTTTCTACAGACAAGAAAAGGGCGACTCATCAGTCGCCTTAAATATCCGTTTGTCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcat                                                                                     <  2:789130‑M1/141‑40 (MQ=255)                                        atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTATACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttctgtcatca                                                                                   >  2:123254‑M1/1‑102 (MQ=255)                                            ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactac                                                                               <  2:868037‑M1/143‑46 (MQ=255)                                             gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAACAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacg                                                                              <  1:757536‑M1/143‑47 (MQ=255)                                              ttgcatgCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgt                                                                             <  1:746251‑M1/140‑48 (MQ=255)                                                tcgtgccGTCGCTCCTCATCTTACTTGTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttc                                                                           <  1:392808‑M1/140‑50 (MQ=255)                                                tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgggcccgtcttcggtcatcactccgttc                                                                           >  1:597386‑M1/1‑94 (MQ=255)                                                           ctcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgtgcagttcggtgtc                                                                >  1:4117‑M1/1‑83 (MQ=255)                                                            tcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCGTAAAAATCAGTTTGCCAGCGCCGCCTTCTGAcgacccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgttggtcgct                                                               >  1:514760‑M1/1‑82 (MQ=255)                                                                    ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactccgttcatgtcggtctctgcggcaga                                                       >  1:299026‑M1/1‑74 (MQ=255)                                                                        ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtct                                                   >  1:83177‑M1/1‑70 (MQ=255)                                                                        ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtccctgcggcagagcct                                                   >  2:139472‑M1/1‑70 (MQ=255)                                                                            cTACAGACAATTAAATGGCTACTCATCAGTCGCCTTAAAAATCAGGTTGCCAGCGCCGCCTACTGCagttcccggcagttcaatgctgcgcgcgtcttctgtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                               <  1:83931‑M1/143‑78 (MQ=255)                                                                            cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                               <  1:421397‑M1/143‑78 (MQ=255)                                                                             tACAGGCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcctgtcgggctcttcgccagggccttcaac                                              >  2:235365‑M1/1‑65 (MQ=255)                                                                             tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgtgcaggtcggtctctgcggtagagtcttcagc                                              >  1:92348‑M1/1‑65 (MQ=255)                                                                              aCAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacg                                             >  1:113925‑M1/1‑64 (MQ=255)                                                                                       aaaagGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccaga                                    <  2:768167‑M1/143‑89 (MQ=255)                                                                                        aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttaaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                   <  1:86244‑M1/143‑90 (MQ=255)                                                                                         aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCGGCcgtcccctgcatttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatc                                  <  1:858276‑M1/143‑91 (MQ=255)                                                                                          aaGGCGCCCCACCAGTCGCCGTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcctgtcggtctctgcggcagagtcttcaacgtattccagatcg                                 <  2:499396‑M1/143‑92 (MQ=255)                                                                                             gCGACTCATCAGTCGTCTTAAAGAGCTGGTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccttcttcggtcatgactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaa                              <  2:415783‑M1/143‑95 (MQ=255)                                                                                               gACGCAGCAGTCGCATTAAAAATGAGTTGGCCCGCGCCGCCTCCTGCcgtcccctgcacttcaatgatgcgcacgtcatcggtcagcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaac                            <  1:340178‑M1/143‑97 (MQ=255)                                                                                                cctgatcaggcgCGTGAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcactgcaatgatgcgcccgtcttcggtcagcactacgttcatgtcggtctctgcggcagggtcttcaacgtattccagatcgcaaacc                           <  2:447776‑M1/139‑98 (MQ=255)                                                                                                 cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcgctacgttcatgtcggtctctgcggccgagtcttcaacgtattcgcgatcgcacacgg                          >  1:180942‑M1/1‑45 (MQ=255)                                                                                                    atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactccgttcatgtcggtctctgcggccgagtcttcaacgtattccagagcgcaaaccgctg                       >  1:27649‑M1/1‑42 (MQ=255)                                                                                                    atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgctt                       >  1:734337‑M1/1‑42 (MQ=255)                                                                                                        gTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcacgtcggtctctgcgccagagtcttcaacggattccagctcgcaaaccgctacgcc                   >  2:448715‑M1/1‑38 (MQ=255)                                                                                                         tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcactgcaatggtgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccg                  <  1:33285‑M1/143‑107 (MQ=255)                                                                                                            tctgaaaaatcagTTTGCGAGCGCCGTCTTCGGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttc               <  1:682088‑M1/139‑110 (MQ=255)                                                                                                              ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcac             >  1:170425‑M1/1‑32 (MQ=255)                                                                                                              ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatacgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtattcaacgtagtccagatcgcaaaccgcttcgcaggtcac             >  1:274264‑M1/1‑32 (MQ=255)                                                                                                                aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaa           <  1:289650‑M1/143‑114 (MQ=255)                                                                                                                    aTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgccaaccgcttcgccgttcacagttcc       >  1:885164‑M1/1‑26 (MQ=255)                                                                                                                    aTCAGTTTGCCAGCGCCGACTTCTGCagtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcgtcaacgtattccagatcgcaaaccgcatcgacgttcacaagtcc       >  2:20827‑M1/1‑26 (MQ=255)                                                                                                                       agttgtccagggccGCCGTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgtgcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac    <  2:243563‑M1/137‑121 (MQ=255)                                                                                                                         tttGCCAACGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgtgcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgtgcacaagtccgacag  >  1:532294‑M1/1‑21 (MQ=255)                                                                                                                                             |                                                                                                                           CACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATC  >  NC_000913/3815718‑3815980

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: ‑