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	43 [0]	[0] 43	[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)	39 (1.140)	31/264	0.1	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

ACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTC  >  NC_000913/3815717‑3816000                                                                                                                                               |                                                                                                                                               acacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCc                                                                                                                                               <  1:576090‑M1/143‑2 (MQ=255)   tcctGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTTATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgt                                                                                                                                             <  2:125099‑M1/142‑4 (MQ=255)      tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                          <  1:423333‑M1/143‑7 (MQ=255)      tgcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCCTCGCTCCTCTTCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                          <  1:383488‑M1/143‑7 (MQ=255)       gcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTACCAGCGCCGCCTTCTGCcgtcccc                                                                                                                                         >  2:421834‑M1/1‑136 (MQ=255)        cttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccct                                                                                                                                        <  2:546495‑M1/143‑9 (MQ=255)           gctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgca                                                                                                                                     <  2:150470‑M1/143‑12 (MQ=255)             tAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTACcgtaccctgcact                                                                                                                                   >  2:565552‑M1/1‑130 (MQ=255)                  gcAAATTCAATAAACTGTCGCTTATATGGTGTCATGCCTTCGCTCCTCATCTTACTATTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                              <  2:326053‑M1/143‑19 (MQ=255)                                  ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcg                                                                                                              <  1:101001‑M1/143‑35 (MQ=255)                                  gccgctgATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcg                                                                                                              <  1:202626‑M1/141‑35 (MQ=255)                                     gcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatcatgcgcccgtcttcggcc                                                                                                           >  1:457353‑M1/1‑106 (MQ=255)                                            tGGTATCATGCCTTCGCTCCGCATCTTACGTGTCTACAGAC‑AAAAAAAAGGCGACTCAGCAGTCGCCTTAAAAATCAGTCTGCCAGCGCTGCGTTCGGCtggcccctgcacttcaatgatgcgcccgtcttcggtcatcacta                                                                                                    <  2:300737‑M1/143‑45 (MQ=255)                                             ggTTTCATGCCTGCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactac                                                                                                   <  1:377094‑M1/143‑46 (MQ=255)                                               tttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAACAAGGCGCCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcctccggcaccaccacgt                                                                                                 >  2:158451‑M1/1‑96 (MQ=255)                                                       cTTCGCACCTCATCTTACTTCTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaaagaagcgcccgtcttcggtcatcactacgttcatgtcg                                                                                         <  2:609204‑M1/143‑56 (MQ=255)                                                              cctcATCTTACTTTTCTACAGACAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtacct                                                                                   >  2:173007‑M1/1‑82 (MQ=255)                                                                taatcTTACTGTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttccatgatgcgcccgacttcggtcctcactacgctcatgtcggtctctgcg                                                                                >  2:174073‑M1/3‑79 (MQ=255)                                                                   tCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccactgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtgtctgcggca                                                                             >  1:362791‑M1/1‑76 (MQ=255)                                                                    cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcag                                                                            >  1:424829‑M1/1‑75 (MQ=255)                                                                     ttcctttTCTACAGGC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTCTGCCAGCGCCGCCTTCTGCcggcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                           <  1:13247‑M1/140‑70 (MQ=255)                                                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtctcctgcacttcaatgatccgcccgtcttccgtcaccgctacgttccttgcggtccccgcggccgccact                                                                       >  1:204227‑M1/1‑70 (MQ=255)                                                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctccgcggcagcgtcc                                                                       >  1:272409‑M1/1‑70 (MQ=255)                                                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacggtcatgtcgctctctgccgcagaggcg                                                                       >  2:345649‑M1/1‑70 (MQ=255)                                                                         ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtctccggtcctcactacgttcatgtcgcgctctgcggcagagtct                                                                       >  2:377732‑M1/1‑70 (MQ=255)                                                                           ttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagccttc                                                                     >  1:529669‑M1/1‑68 (MQ=255)                                                                             ctacctac‑aaaaaAAAGGCGACTCATCAGTCGCCTTAAAAAGCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                                                   <  1:450975‑M1/137‑78 (MQ=255)                                                                             cTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgtccatgtcggtctctgcggcagggtcttcaa                                                                   >  1:155194‑M1/1‑66 (MQ=255)                                                                              tACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcacc                                                                  >  2:304666‑M1/1‑65 (MQ=255)                                                                                 aGAC‑AAAAAAAGGGCGACGCATCGGGCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgta                                                               <  2:230119‑M1/143‑82 (MQ=255)                                                                                       tttttaaggcgaCTGATGAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggccatcactacgctcatgtcggtctctgcggcggtgtcttcaacgtactcca                                                          >  1:97942‑M1/6‑57 (MQ=255)                                                                                       ataaaaaggCGCCTCATCAGTCGCCTTAATGATCCGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattcca                                                          <  2:72215‑M1/141‑87 (MQ=255)                                                                                          aaacGGCGCCTCATCTCTCGCCTTAAACATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgctgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                       <  2:318677‑M1/143‑90 (MQ=255)                                                                                           aaaGGCGATTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatc                                                      <  2:537119‑M1/143‑91 (MQ=255)                                                                                           aaaGGCGACTCATCAGTCGTGTTAGAGTTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatc                                                      <  1:519086‑M1/143‑91 (MQ=255)                                                                                                 gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagcattcaacgcattccagatcgcaaac                                                >  2:53127‑M1/1‑47 (MQ=255)                                                                                                          gTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggccgagtcttcaacgtattccagatcgcaaaccgcttcccc                                       >  1:166901‑M1/1‑38 (MQ=255)                                                                                                                ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcac                                 >  1:403868‑M1/1‑32 (MQ=255)                                                                                                                                cAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcaccattccgccagaaact                 >  1:657375‑M1/1‑16 (MQ=255)                                                                                                                                      cgctTTCTGCtgtcccctgcacttcaatgatgcgcacgtattcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggct           <  1:287303‑M1/143‑134 (MQ=255)                                                                                                                                      cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcgggcctcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagagcgcaaaccgctgcgccgtctccacttccgccagaacctggggcg           >  2:290416‑M1/1‑10 (MQ=255)                                                                                                                                        ccTTCTGCcgtcccatgcacttcagtgatggtcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctac         <  2:217929‑M1/143‑136 (MQ=255)                                                                                                                                               ccgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcacaccgcttcgccgttcacaattccgacagaaactgcggctaccatccct  >  2:646324‑M1/1‑1 (MQ=255)                                                                                                                                               |                                                                                                                                               ACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTC  >  NC_000913/3815717‑3816000

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: ‑