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

CAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCC  >  NC_000913/3815800‑3816080                                                                                                                                              |                                                                                                                                            cacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgccc                                                                                                                                            >  1:540551‑M2/142‑142 (MQ=255) cacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCg                                                                                                                                            <  2:415956‑M2/2‑1 (MQ=255)  cacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGt                                                                                                                                           >  1:542571‑M2/141‑143 (MQ=255)    ctgcttgctaagcgcaaattcaataaactggcgctgagatggtttcatgccttcgctcctcctcttacgtttctacagacaaaaaaaaggcgcctcatcagtcgccgtaaaaatcagtttgcgaggcccgccttctgcCCTcc                                                                                                                                         >  1:285223‑M2/139‑143 (MQ=255)        ttgctaagcgcaaattcaataaactggcgctgataggggctcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTg                                                                                                                                     <  1:298216‑M2/9‑1 (MQ=255)         cgagctaagcgcaaattcaataaactgacgctgatatggtttcatgcattcgctcctcatcttacttttctacagacaaaaaagacgactcatcagtcaccttaaaaatcagtttgccagcgccgcctccagcCGCCCCCTGc                                                                                                                                    >  2:478064‑M2/134‑143 (MQ=255)                cgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCaa                                                                                                                             <  1:253347‑M2/17‑1 (MQ=255)                  caaattcaataaactggcgctgatatggtttcatgccttcgctcgtcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAatg                                                                                                                           <  2:167848‑M2/19‑1 (MQ=255)                          ataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGccc                                                                                                                   >  2:524469‑M2/117‑143 (MQ=255)                                gggcgctgatatggtttcatgccttcgctcctcatcttacgtttctacaggcaaaaaaaaggcgacgcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTACCCTGCACTTCAATGATGCGCCCGTCTTc                                                                                                             <  2:701958‑M2/33‑1 (MQ=255)                                   cgcttagatggttgcatgccttctctcctcatcttacttttctacagacaaaaaaaaggcgactcatcaggcgccttaaaaatcagtctgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                                                                                          <  2:230452‑M2/36‑1 (MQ=255)                                      tcatatggtttcatgcctcccccccgcatctcacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                                                                                       <  1:187189‑M2/39‑1 (MQ=255)                                      cgatatggtgtcatgccttcgcacctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                                                                                       <  1:112812‑M2/39‑1 (MQ=255)                                          atggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCCATGATGCGCCCGTCTTCGGTCATCACt                                                                                                   >  1:713762‑M2/101‑143 (MQ=255)                                           tggtttcatgccttcgcgcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                                                                                                  <  1:388453‑M2/44‑1 (MQ=255)                                                  atgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaacaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCCTCTTCGGTCCTCCCTCCGTTCAt                                                                                           >  1:124412‑M2/93‑143 (MQ=255)                                                    gccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCATTGATGCGCCCGCCTTCGGTCGTCACTACTTGCATGt                                                                                         >  1:657740‑M2/91‑143 (MQ=255)                                                     ccgtcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttggcagcgccgccttctgtCGTCCCCTGCACTTGAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTc                                                                                        <  2:15567‑M2/54‑1 (MQ=255)                                                       ttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTCCGTTCATGTCgg                                                                                      >  1:548784‑M2/88‑143 (MQ=255)                                                                  ttttacttttctacagataaaaaagaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccgtctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGTTCATCACTACGCTCATGTCGGTCTCTGCGGCa                                                                           <  2:373873‑M2/67‑1 (MQ=255)                                                                    ttgcttttctacagacaaacaataggcgactcatcagtcgccttaaacatcattttgccagcgccgccctctgaCGTCCTCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                                         <  2:9349‑M2/69‑1 (MQ=255)                                                                    ctacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgcctgctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTTCGTTCATGTCGGTCTCTGCGGCaga                                                                         <  1:217943‑M2/69‑1 (MQ=255)                                                                                  acaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGCCTTCAACGTatg                                                           >  2:544948‑M2/61‑142 (MQ=255)                                                                                     aaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTTCGGCAGAGTCTTCATCGTAttcaa                                                        >  1:54086‑M2/58‑141 (MQ=255)                                                                                       aaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTCCGTTCCTGTCGGTCCCTGCGGCAGACTCTTCAACGTATTacacc                                                      >  2:53394‑M2/56‑141 (MQ=255)                                                                                        aaaaggctgctcatcagtcgccttaagaatcagttttccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                     <  2:506327‑M2/89‑1 (MQ=255)                                                                                        aaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                     <  1:587057‑M2/89‑1 (MQ=255)                                                                                                        gtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCAGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGcc                                     <  2:709893‑M2/105‑1 (MQ=255)                                                                                                              ttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCAAGATCGCAAACCGCTTCGCCGTTcac                               >  1:460897‑M2/33‑143 (MQ=255)                                                                                                              tcaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTcac                               <  1:471471‑M2/111‑1 (MQ=255)                                                                                                                aaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGttcacca                             >  1:468454‑M2/31‑141 (MQ=255)                                                                                                                aaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACaa                             <  1:524469‑M2/113‑1 (MQ=255)                                                                                                                  aaatcagtttgccagcgccgccttctgcCGTCCCCTACACTCCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAtt                           <  1:363537‑M2/115‑1 (MQ=255)                                                                                                                   aatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACACTTc                          >  2:199370‑M2/28‑143 (MQ=255)                                                                                                                    atcagtttgccagcgccgccttctgcCGTCCTCAACAACTGATGGAAGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGCTCTCTGCGCCAGAGGCTTCAACGTATTCTAGATCGCAAACCGCTTCGCCGTTCACCATTcc                         >  2:624989‑M2/27‑143 (MQ=255)                                                                                                                    atcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCCTCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAAATGGCAAACCGCTTCGACGTTCACAATTcc                         >  1:656356‑M2/27‑143 (MQ=255)                                                                                                                          ttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGa                   >  1:395152‑M2/21‑143 (MQ=255)                                                                                                                                    cgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCAAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCt         >  2:399046‑M2/11‑143 (MQ=255)                                                                                                                                           tgcCGTCCCCTGCATGTCGTTGATGCGCCCGTCTTCGGTCATCACTACGTTCCTGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGTTCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATcc  <  2:549487‑M2/140‑1 (MQ=255)                                                                                                                                              |                                                                                                                                            CAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCC  >  NC_000913/3815800‑3816080

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: ‑