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	54 [0]	[0] 52	[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)	50 (0.730)	32/276	0.8	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

TCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCG  >  NC_000913/3815792‑3816089                                                                                                                                                      |                                                                                                                                                      aactttaacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCg                                                                                                                                                      <  2:491944‑M2/2‑1 (MQ=255) aactttaacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCg                                                                                                                                                      <  1:955727‑M2/2‑1 (MQ=255)      taacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑cccc                                                                                                                                                <  2:940010‑M2/7‑1 (MQ=255)           cctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCa                                                                                                                                            >  1:808176‑M2/140‑150 (MQ=255)                ttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCaa                                                                                                                                      <  1:588304‑M2/17‑1 (MQ=255)                 tgctaagcgcaaattcaataaactggcgctgatatgggttcatgcctgcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaacaatcagtttgccagctccgccttctgcCGT‑CCCCTGCACTTCAat                                                                                                                                     >  2:50781‑M2/134‑151 (MQ=255)                   ctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAatga                                                                                                                                   <  1:747113‑M2/20‑1 (MQ=255)                   ctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAatga                                                                                                                                   <  1:369351‑M2/20‑1 (MQ=255)                   ctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAatga                                                                                                                                   <  1:1007640‑M2/20‑1 (MQ=255)                         gcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATgcgc                                                                                                                              >  1:49891‑M2/126‑150 (MQ=255)                          caaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGccc                                                                                                                            <  1:15412‑M2/27‑1 (MQ=255)                          caaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGcc                                                                                                                             >  1:548463‑M2/125‑150 (MQ=255)                            aattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGt                                                                                                                          >  1:822284‑M2/123‑151 (MQ=255)                                caataaactggcgctgatatgttttcatgccttcgctcctcatcttacttgtctacagacaaaaaaaaggcgactcatcggtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGc                                                                                                                                             <  2:476869‑M2/10‑1 (MQ=255)                                caataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggggactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCtt                                                                                                                       >  2:830259‑M2/119‑150 (MQ=255)                                caataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGc                                                                                                                                             >  1:477070‑M2/119‑128 (MQ=255)                                  ataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgcctgctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTGTTCgg                                                                                                                    <  2:418589‑M2/35‑1 (MQ=255)                                     aactggcgctgatatggtttcatgccttcgttcctcatcttacttttctacagacaaaaaaaaggcgactcattagttgccttaaaaatcagattgccagagccgtcttctgcCGT‑CCCCTGAACTTCAATGATGTGCCCGTCTTTGGtca                                                                                                                 >  2:1152348‑M2/114‑151 (MQ=255)                                     aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCAc                                                                                                                                           >  2:413856‑M2/114‑125 (MQ=255)                                     aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCAc                                                                                                                                           <  1:414013‑M2/12‑1 (MQ=255)                                     aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                                                                                                 <  2:342398‑M2/38‑1 (MQ=255)                                          gcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                                                                                             <  1:43909‑M2/42‑1 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaatgcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACCACGt                                                                                                        >  2:234200‑M2/104‑150 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                                                                                                       >  1:279326‑M2/104‑151 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                                                                                                       >  1:103898‑M2/104‑151 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                                                                                                       >  1:820478‑M2/104‑151 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                                                                                                       >  1:632091‑M2/104‑151 (MQ=255)                                               gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGACCGTCTTCGGTCATCACTACg                                                                                                         >  2:872928‑M2/104‑149 (MQ=255)                                               gatatggtttcatgccttcgctcctcatctaacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCTCCCGTCTTCGGTCATCACTACGtt                                                                                                       >  2:376622‑M2/104‑151 (MQ=255)                                                     gtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGt                                                                                                  <  1:905649‑M2/53‑1 (MQ=255)                                                                   ctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa                                                                                    >  1:99802‑M2/84‑151 (MQ=255)                                                                   ctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag                                                                                   >  1:719286‑M2/84‑151 (MQ=255)                                                                     cctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCagag                                                                                 <  2:403537‑M2/70‑1 (MQ=255)                                                                        catcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt                                                                              <  1:1146001‑M2/73‑1 (MQ=255)                                                                             tacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAGTGATGCGCCCGTCTTCGGTCATCACTACGTTCATTTCGGTCTCTGCGGCAGAGTCTTCAAc                                                                         <  2:369702‑M2/78‑1 (MQ=255)                                                                               cttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGt                                                                       <  2:741902‑M2/80‑1 (MQ=255)                                                                               cttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGt                                                                       <  1:15579‑M2/80‑1 (MQ=255)                                                                               ctttgcgccagacaaaaaaaaagcgactcatcagtcgccttaaaaatcagtgtgccagcgccgccttctgcCGG‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCTCTACGTTCATGTCGGTCTCTGCGGCAGAATCATCaactt                                                                       <  2:752031‑M2/80‑3 (MQ=255)                                                                               attatatacagacaggcaaaaggcgccacaacagtcgccataaaaatcagtttgccagcgccgacttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGt                                                                       <  2:131958‑M2/80‑1 (MQ=255)                                                                                   tctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAtt                                                                    >  1:520922‑M2/68‑150 (MQ=255)                                                                                                aaaaggcgactcatcagacgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAAcc                                                      <  2:979735‑M2/97‑1 (MQ=255)                                                                                                       gactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCg                                                >  1:1097931‑M2/48‑150 (MQ=255)                                                                                                        actcatcagtcgccttaaaaatcagtttgccggcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGc                                               <  1:80084‑M2/104‑1 (MQ=255)                                                                                                        actcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGC‑CTCCTGCACTTCAATGATGCCCCCGCCTTCGGTCATCACCACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGc                                               >  2:809763‑M2/47‑150 (MQ=255)                                                                                                        acgccacagtcgacttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGGATTCCAGATCGCAAACCGCTTCGc                                               <  1:1152893‑M2/104‑1 (MQ=255)                                                                                                                 tcgccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTcaca                                       <  2:498343‑M2/112‑1 (MQ=255)                                                                                                                    ccttaaaaatcagtttgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTc                                   >  1:984929‑M2/35‑150 (MQ=255)                                                                                                                              tccgtataatgcgccgccttctgcCGT‑CCCCTGCCCTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAAc                         <  1:686300‑M2/126‑1 (MQ=255)                                                                                                                                   tgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCgg                    >  1:982634‑M2/20‑150 (MQ=255)                                                                                                                                   tgccagcgccgccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCgg                    >  1:92624‑M2/20‑150 (MQ=255)                                                                                                                                             nccttctgcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATcc           >  1:317800‑M2/10‑149 (MQ=255)                                                                                                                                                    gcCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCg  >  1:991429‑M2/3‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                      TCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCG  >  NC_000913/3815792‑3816089

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑