Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1299499–1300697	1300697	1–1199	58 [0]	[0] 59	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1299498	0 (0.000)	56 (1.380)	53/276	0.0	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

CAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTC  >  NC_000913/1299362‑1299638                                                                                                                                         |                                                                                                                                             cAGTTAGTTATATGGATTTCCCTAACGGCTTCTCCGCACCTTCATGTTATTTTCGCCACATCATAATCCTGGGCTCGCTGCAGGATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                        <  2:229375‑M1/143‑7 (MQ=255)  agttagttATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCATGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTACCTTTGGTAGAGGAAAGTGCTAAataataa                                                                                                                                       >  2:45462‑M1/1‑136 (MQ=255)        ttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTATAGGAAAGTGCTAAataataatcaatt                                                                                                                                 <  2:561796‑M1/143‑14 (MQ=255)          ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTACataataatcaattgt                                                                                                                               >  2:405228‑M1/1‑128 (MQ=255)           taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAGGTGCTAAataataatcaattgtt                                                                                                                              >  1:419597‑M1/1‑127 (MQ=255)              ggATTTCCTTAACTGCTTCTCCTCACCATCATGTTATCTTCGCCACATCATACTCCTGGCCTTGCTGAAGAATAATTGAAATGATATTATTAATCCCACTGCCTTTGGAATAAGAAAGCACTAAataatcatcaatttttagc                                                                                                                           >  2:595074‑M1/1‑124 (MQ=255)                aTTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaatt                                                                                                                         >  1:460289‑M1/1‑122 (MQ=255)                 tttCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaatta                                                                                                                        <  1:364700‑M1/143‑23 (MQ=255)                      ttAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtg                                                                                                                   >  1:107920‑M1/1‑116 (MQ=255)                      gtaACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGATAAatcataatcaattgttaaattattgtg                                                                                                                   <  2:637856‑M1/142‑28 (MQ=255)                        aaCTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAACCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgca                                                                                                                 <  1:298019‑M1/143‑30 (MQ=255)                         aCTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCCCTGCCTTTGGTAGAGCAAAGTGCTAAataataatcaattgttaaattattgtgcat                                                                                                                >  2:330042‑M1/1‑113 (MQ=255)                             cTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttca                                                                                                            >  2:420284‑M1/1‑109 (MQ=255)                              ttCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcac                                                                                                           <  2:369944‑M1/143‑36 (MQ=255)                              ttCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataagcaattgttaaattattgtgcatttcac                                                                                                           >  1:502682‑M1/1‑108 (MQ=255)                               tctcCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcact                                                                                                          >  1:3413‑M1/1‑107 (MQ=255)                                ctcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTTCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcacta                                                                                                         <  1:118457‑M1/143‑38 (MQ=255)                                   ctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGCAGAATAATTGAAATGGTAGTATTAGTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattcttcaattatagtgcatttcactactc                                                                                                      >  2:352167‑M1/1‑103 (MQ=255)                                    tcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAAAGACAAGCGCTAAttaataatacatggtcaaattattgtgcatttcactactgg                                                                                                     >  2:117502‑M1/1‑102 (MQ=255)                                      aCCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                   <  1:672772‑M1/143‑44 (MQ=255)                                            atGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaa                                                                                             >  2:692724‑M1/1‑94 (MQ=255)                                             tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCCCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattatgcatttcactactggaactgtaaa                                                                                            >  2:289892‑M1/1‑93 (MQ=255)                                              gTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatc                                                                                           >  1:691789‑M1/1‑92 (MQ=255)                                              gTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatc                                                                                           <  2:152373‑M1/143‑52 (MQ=255)                                                tATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactcgaactgtaataag                                                                                         >  2:263309‑M1/1‑90 (MQ=255)                                                 aTTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttacattttggtgcatttcactactggaactgtgctcaga                                                                                        >  1:132631‑M1/1‑89 (MQ=255)                                                  atgtcgcAACATCATAATCCTGGGCAAGCAGAAAAATAATTGAAATGATATTATAAATTCCACTGCCTTTGGTAGAGGAAAGGGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaa                                                                                       <  2:474357‑M1/140‑56 (MQ=255)                                                       gCCATATCATAATCCTGGGTTTGCTGAATAATAATTGACATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagat                                                                                  <  2:2848‑M1/143‑61 (MQ=255)                                                        caacatcATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagata                                                                                 <  2:218948‑M1/141‑62 (MQ=255)                                                         cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAGataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatag                                                                                <  1:317339‑M1/143‑63 (MQ=255)                                                              catAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGACTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatg                                                                           >  2:243762‑M1/1‑76 (MQ=255)                                                               atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                          >  2:65476‑M1/1‑75 (MQ=255)                                                                  aTCCTGGGCTTGCTGAAGAATAATTGAAATGATATTACTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                       <  1:133487‑M1/143‑72 (MQ=255)                                                                    ccTGGGCTTGCTGAAGAATAATTCAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagc                                                                     <  1:34592‑M1/143‑74 (MQ=255)                                                                       gggCTTGCTGAAGAATAAGTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAagaataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaa                                                                  <  2:201040‑M1/143‑77 (MQ=255)                                                                               tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatc                                                          >  1:665277‑M1/1‑59 (MQ=255)                                                                               tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagaaatgcttagccaatctctatt                                                          >  1:695754‑M1/1‑59 (MQ=255)                                                                                tacgaataaGTGAAATGATATTATTATTTCCACGGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                         <  2:144049‑M1/140‑86 (MQ=255)                                                                                        atTGAAATGTTCTTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaat                                                 <  2:300191‑M1/143‑94 (MQ=255)                                                                                        atTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaat                                                 <  2:370295‑M1/143‑94 (MQ=255)                                                                                          tGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattg                                               >  1:97810‑M1/1‑48 (MQ=255)                                                                                            aaaTGATATTATTAATTCCACTGCTTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaa                                             <  2:425836‑M1/143‑98 (MQ=255)                                                                                             aaTTATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaa                                            <  2:30381‑M1/143‑99 (MQ=255)                                                                                             aaTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaa                                            >  1:177251‑M1/1‑45 (MQ=255)                                                                                                          atgccactGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaag                               <  1:632069‑M1/140‑112 (MQ=255)                                                                                                             ccACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggca                            <  2:350870‑M1/143‑115 (MQ=255)                                                                                                               aCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatg                          >  1:218659‑M1/1‑27 (MQ=255)                                                                                                                  gCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatccgaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggat                       <  2:363593‑M1/143‑120 (MQ=255)                                                                                                                    cTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgc                     >  2:616672‑M1/1‑22 (MQ=255)                                                                                                                            gagGAAAGTGCTGAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttacggcatggatgcaagctata             <  1:12936‑M1/143‑130 (MQ=255)                                                                                                                             agGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatag            >  1:293210‑M1/1‑13 (MQ=255)                                                                                                                              ggAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactataatcagaaaagatatacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctataga           <  2:47950‑M1/143‑132 (MQ=255)                                                                                                                               gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagat          >  1:439332‑M1/1‑11 (MQ=255)                                                                                                                                 gagTGCTAAataataatcaattgttaaattattgtgcatttcacgactggaactgtaatcagagaagatagacaggcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattc        <  2:143837‑M1/142‑135 (MQ=255)                                                                                                                                    tGCTAActaataataaattgtgcaatttgtctccattccacgactggaactgtaatcagaaaagatagacatgcttagacaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagatcctga     <  1:366930‑M1/143‑138 (MQ=255)                                                                                                                                    tGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctga     <  1:294549‑M1/143‑138 (MQ=255)                                                                                                                                      cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagacaagatagacatgcttagccaatctctatttgatttaattgaaagatgtttgttaaggcatggatgcaagctatagattctgata   <  2:198199‑M1/143‑140 (MQ=255)                                                                                                                                       tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcacgatatgactgctgatac  >  2:538828‑M1/1‑3 (MQ=255)                                                                                                                                         |                                                                                                                                             CAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTC  >  NC_000913/1299362‑1299638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑