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	34 [0]	[0] 34	[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)	33 (1.330)	31/264	0.0	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

ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCA  >  NC_000913/3815799‑3816077                                                                                                                                               |                                                                                                                                           acacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcc                                                                                                                                            <  2:387610‑M2/1‑1 (MQ=255)    cctgcttgctaagcgcaaattcaataaactggcgctgatatggcttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgtctcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTc                                                                                                                                         <  1:359320‑M2/4‑1 (MQ=255)     ctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTcc                                                                                                                                        >  1:388122‑M2/139‑143 (MQ=255)      tgcttgcaaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTccc                                                                                                                                       <  1:476166‑M2/6‑1 (MQ=255)            ctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCAc                                                                                                                                 >  1:319114‑M2/132‑143 (MQ=255)                  gcaaattcagtaagctggcgctgatatggtttcatgacttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAat                                                                                                                          <  2:327402‑M2/18‑1 (MQ=255)                  gcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatccgtttgccagctccgccttctgcCGTCCCCTCCACTT‑CAat                                                                                                                          >  1:128896‑M2/126‑143 (MQ=255)                     aattcaataacctggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAatgat                                                                                                                       <  2:188483‑M2/21‑1 (MQ=255)                     aattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAatgat                                                                                                                       <  2:131463‑M2/21‑1 (MQ=255)                       ttcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttacaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCCAatgatg                                                                                                                      >  2:18407‑M2/121‑143 (MQ=255)                       ttcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGGCCCCTGCACTT‑CAACAATgc                                                                                                                     >  2:139093‑M2/121‑143 (MQ=255)                              aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTc                                                                                                              <  1:30554‑M2/30‑1 (MQ=255)                                ctggggcggatattgtgtcgtgccttccctcctcatgttacttttctacaggaataaaaaaggcggctcatcagtcgccttaaaaatctgtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCTGTCtt                                                                                                            <  2:40451‑M2/32‑1 (MQ=255)                                    ccctgctatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGt                                                                                                        <  2:201136‑M2/36‑1 (MQ=255)                                        gatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGtcatc                                                                                                    >  1:100949‑M2/104‑143 (MQ=255)                                                      ccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTc                                                                                     <  1:42227‑M2/54‑1 (MQ=255)                                                            ctccgcatcttacttttcgacagacaaaaacaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGtctc                                                                               <  2:63386‑M2/60‑1 (MQ=255)                                                               ctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGGCTCTGc                                                                            >  1:111974‑M2/81‑143 (MQ=255)                                                                tcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCGCGTCTTCGGTCAGCACTAC‑GTTCATGTAGGTCTCTgca                                                                           >  1:15572‑M2/80‑142 (MQ=255)                                                                          ttttctacagacaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGCCtt                                                                 >  1:319153‑M2/70‑143 (MQ=255)                                                                          cgtatacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                 <  1:84593‑M2/74‑1 (MQ=255)                                                                                   acaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCCCTAC‑GCCCATGTCGGTCTCTGCGGCAGAGGCTTCAACGTGtt                                                        >  2:468507‑M2/61‑143 (MQ=255)                                                                                   acaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAtt                                                        <  1:36170‑M2/83‑1 (MQ=255)                                                                                    caaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                       <  1:397275‑M2/84‑1 (MQ=255)                                                                                     aaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCAGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCATCAACGTATTcc                                                      >  1:370304‑M2/59‑143 (MQ=255)                                                                                        aaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTCCATGTCGGTCTCTGCGCCCCAGTCTCCATCGTATTCCAGa                                                   >  2:362129‑M2/56‑143 (MQ=255)                                                                                                     atcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGGCTAAGGTCAAC‑CAACAGTGTATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCTAGATCGCAAGCGGCtt                                      >  1:111209‑M2/43‑143 (MQ=255)                                                                                                      tcagtcgccttaaaaatcagtgtgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTGCGGGCAGCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTc                                     <  1:278190‑M2/102‑1 (MQ=255)                                                                                                       cagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑CTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCg                                    <  1:237689‑M2/103‑1 (MQ=255)                                                                                                                  ataatcagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCAGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAt                         <  1:70853‑M2/114‑1 (MQ=255)                                                                                                                   aaatcagtttgccagcgccggcttatgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACGAC‑GGTCATGCCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCCGATCGCAAACCGCTTCGCCGTTCACAAtt                        <  1:313482‑M2/115‑1 (MQ=255)                                                                                                                       cagtttgccagcgccgccttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATAACTAC‑AATCATGTAGGTCTCTGCGACAGAGCCTTCAACGTATTCCAGATAGCAAACCGCTTCGCCGTTCACAAttccaa                    >  1:476560‑M2/25‑141 (MQ=255)                                                                                                                                  cgccgccttctccCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAACCCGCTTCGCCATTCACAATTCCGACAGAAACTGCg         <  2:355770‑M2/130‑1 (MQ=255)                                                                                                                                         ttctgcCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GCTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCa  >  1:260947‑M2/7‑143 (MQ=255)                                                                                                                                               |                                                                                                                                           ACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTT‑CAATGATGCGCCCGTCTTCGGTCATCACTAC‑GTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCA  >  NC_000913/3815799‑3816077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑