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

AACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACT  >  NC_000913/3815716‑3815983                                                                                                                                               |                                                                                                                              aaCACCTGCGTGCTAAGCGCTAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGC                                                                                                                               <  2:213699‑M1/143‑1 (MQ=255)  acacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCc                                                                                                                              <  1:545088‑M1/143‑2 (MQ=255)    acCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgt                                                                                                                            <  1:80117‑M1/143‑4 (MQ=255)     tctGCTTGCTAAGCGCAAAGTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtc                                                                                                                           <  2:410837‑M1/142‑5 (MQ=255)     ccTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTGTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAGTCAGTTTGCCCGCGCCTCCTCCTGCcgtg                                                                                                                           >  2:39831‑M1/1‑139 (MQ=255)      cTGCTTGCTACGCGTAAACTCAATAATCTGGCGCTGATATCGTTTCATGCCTTCGCTCCTCGTCTTACCTGTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcc                                                                                                                          <  2:391238‑M1/143‑6 (MQ=255)        gcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCGACAGACAAAAAAAAGGCGACTCATCAGTCCCCTTACAAATCAGTTTGACAGCGCCGCCTTCTGCcgacccc                                                                                                                        >  2:149621‑M1/1‑136 (MQ=255)          ttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctg                                                                                                                      <  1:638863‑M1/143‑10 (MQ=255)                  cgcAAATTCAATACACGAGCTTGGAGATAGTTTCATGCCTTCGCGCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                              <  2:114490‑M1/143‑18 (MQ=255)                  cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTATCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGAcctcccctgcacttcac                                                                                                              >  2:363336‑M1/1‑126 (MQ=255)                      aaTTCAAGAACCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCGAGCGCCGCCTTCTGCcgtcccctgcacttcaatgat                                                                                                          <  1:473668‑M1/143‑22 (MQ=255)                                    gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTCCAGACAAAAAAAAGGCGCCTCCTCAGTAGCCTTACAAATCAGTGTGCCCGCGACGCCTTATGCcgtcccctgcacttcaatgatgcgcccgcagtcga                                                                                            >  2:715915‑M1/1‑108 (MQ=255)                                        tGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcat                                                                                        >  2:196463‑M1/1‑104 (MQ=255)                                                tttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtaccctgcacttcaatgatgcgcccgtcttcaggcaccactacgt                                                                                >  2:483038‑M1/1‑96 (MQ=255)                                                  gcctgccTTCGCCGCTCCTCTTGCTTTTCTACAGACAACAAAAAGGCGCCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttc                                                                              <  2:509536‑M1/140‑50 (MQ=255)                                                        ctgcgcgcctCATCCTACGTTCCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCCGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcg                                                                        <  1:552312‑M1/140‑56 (MQ=255)                                                                    tCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTATGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgctcatgacggtctcgtcggca                                                            >  2:142173‑M1/1‑76 (MQ=255)                                                                      ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                          <  1:36903‑M1/143‑70 (MQ=255)                                                                         cTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAGCCGGATGCGCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtc                                                       <  1:306801‑M1/143‑73 (MQ=255)                                                                               tagagacATAAGAAGGGCGGCTCGTCTGTCGCCTTAAAAAGCAGTTTGTCAGCGCTGCCTTCTGCcgtcccctgcgcttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaac                                                 <  2:437167‑M1/140‑79 (MQ=255)                                                                               tACAGACAAAAAAAAGGCGACTCATCAGTCGCATTAAAAATCAGTTTGCCACCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaac                                                 >  2:382644‑M1/1‑65 (MQ=255)                                                                                  aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcacctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcgccaggggcttcaacgga                                              >  1:386218‑M1/1‑62 (MQ=255)                                                                                  aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGACAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgctaatgtcggtctctgccgcagagagttcaaccaa                                              >  2:420230‑M1/1‑62 (MQ=255)                                                                                   gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtat                                             <  1:541386‑M1/143‑83 (MQ=255)                                                                                                        caGTCGCCTTAAAACGCAGTTCGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcg                        <  2:702423‑M1/143‑104 (MQ=255)                                                                                                            cGCCTTAAAAATCAGTTTGCCAGCGCCGCCTCCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgt                    <  2:467624‑M1/143‑108 (MQ=255)                                                                                                            cGCCGTAAAAATCAGTGTGCCAGCGCCGCCCTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgt                    <  1:43355‑M1/143‑108 (MQ=255)                                                                                                                     aaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttccacgtattccagatcgcaaaccgcttcgccgttcacaagtc           >  1:543159‑M1/1‑27 (MQ=255)                                                                                                                        cAGTCTGCCAGCGCCGCCTGCGGCcgtccccggcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccga        <  2:726857‑M1/143‑120 (MQ=255)                                                                                                                            ttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcagtctctacggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagc    >  1:413238‑M1/1‑20 (MQ=255)                                                                                                                              gCCCGCGCCGCCTTCTGCcgtcccctgcacttcaatgctgcgcccgtcttcggtcatcactacgttcatgtcggtcgctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaa  <  2:282067‑M1/143‑126 (MQ=255)                                                                                                                                               |                                                                                                                              AACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACT  >  NC_000913/3815716‑3815983

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: ‑