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	31 [0]	[0] 30	[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)	30 (0.800)	28/262	0.3	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

ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAA  >  NC_000913/3815799‑3816065                                                                                                                                               |                                                                                                                             acacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcc                                                                                                                              <  1:545088‑M2/1‑1 (MQ=255)   acctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGt                                                                                                                            <  1:80117‑M2/3‑1 (MQ=255)    tctgcttgctaagcgcaaagtcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTc                                                                                                                           <  2:410837‑M2/4‑1 (MQ=255)    cctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttgtctacagacaaaaaaaaggcgactcatcagtcgccttaaaagtcagtttgcccgcgcctcctcctgcCgtg                                                                                                                           >  2:39831‑M2/140‑142 (MQ=255)     ctgcttgctacgcgtaaactcaataatctggcgctgatatcgtttcatgccttcgctcctcgtcttacctgtctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTcc                                                                                                                          <  2:391238‑M2/5‑1 (MQ=255)       gcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttcgacagacaaaaaaaaggcgactcatcagtccccttacaaatcagtttgacagcgccgccttctgcCGAcccc                                                                                                                        >  2:149621‑M2/137‑143 (MQ=255)         ttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTg                                                                                                                      <  1:638863‑M2/9‑1 (MQ=255)                 cgcaaattcaatacacgagcttggagatagtttcatgccttcgcgcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCaa                                                                                                              <  2:114490‑M2/17‑1 (MQ=255)                 cgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttatctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgaCCTCCCCTGCACTTcac                                                                                                              >  2:363336‑M2/127‑142 (MQ=255)                     aattcaagaacctggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgcgagcgccgccttctgcCGTCCCCTGCACTTCAatgat                                                                                                          <  1:473668‑M2/21‑1 (MQ=255)                                   gcgctgatatggtttcatgccttcgctcctcatcttacttttctccagacaaaaaaaaggcgcctcctcagtagccttacaaatcagtgtgcccgcgacgccttatgcCGTCCCCTGCACTTCAATGAtgcgcccgcagtcga                                                                                            >  2:715915‑M2/109‑136 (MQ=255)                                       tgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                                                                        >  2:196463‑M2/105‑143 (MQ=255)                                               tttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTACCCTGCACTTCAATGATGCGCCCGTCTTCAGGCACCACTACGt                                                                                >  2:483038‑M2/97‑143 (MQ=255)                                                 gcctgccttcgccgctcctcttgcttttctacagacaacaaaaaggcgcctcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                                                                              <  2:509536‑M2/49‑1 (MQ=255)                                                       ctgcgcgcctcatcctacgttcctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttccgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                                                                        <  1:552312‑M2/55‑1 (MQ=255)                                                                   tcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttatgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGCTCATGACGGTCTCGTCGGCa                                                            >  2:142173‑M2/77‑143 (MQ=255)                                                                     ttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                          <  1:36903‑M2/69‑1 (MQ=255)                                                                        cttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaagccggatgcgcagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc                                                       <  1:306801‑M2/72‑1 (MQ=255)                                                                              tagagacataagaagggcggctcgtctgtcgccttaaaaagcagtttgtcagcgctgccttctgcCGTCCCCTGCGCTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                                 <  2:437167‑M2/78‑1 (MQ=255)                                                                              tacagacaaaaaaaaggcgactcatcagtcgcattaaaaatcagtttgccaccgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                                 >  2:382644‑M2/66‑143 (MQ=255)                                                                                 agacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCACCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGCCAGGGGCTTCAacgga                                              >  1:386218‑M2/63‑141 (MQ=255)                                                                                 agacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgacagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGCTAATGTCGGTCTCTGCCGCAGAGAGTTcaaccaa                                              >  2:420230‑M2/63‑140 (MQ=255)                                                                                  gacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAt                                             <  1:541386‑M2/82‑1 (MQ=255)                                                                                                       cagtcgccttaaaacgcagttcgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCg                        <  2:702423‑M2/103‑1 (MQ=255)                                                                                                           cgccttaaaaatcagtttgccagcgccgcctcctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGt                    <  2:467624‑M2/107‑1 (MQ=255)                                                                                                           cgccgtaaaaatcagtgtgccagcgccgccctctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGt                    <  1:43355‑M2/107‑1 (MQ=255)                                                                                                                    aatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCCACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAGTc           >  1:543159‑M2/28‑143 (MQ=255)                                                                                                                       cagtctgccagcgccgcctgcggcCGTCCCCGGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGa        <  2:726857‑M2/119‑1 (MQ=255)                                                                                                                           ttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCAGTCTCTACGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACagc    >  1:413238‑M2/21‑142 (MQ=255)                                                                                                                             gcccgcgccgccttctgcCGTCCCCTGCACTTCAATGCTGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCGCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGaaa  <  2:282067‑M2/125‑1 (MQ=255)                                                                                                                                               |                                                                                                                             ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAA  >  NC_000913/3815799‑3816065

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: ‑