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	59 [0]	[0] 60	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)	54 (1.380)	45/274	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

ACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT  >  NC_000913/1299361‑1299639                                                                                                                                          |                                                                                                                                              aCAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataat                                                                                                                                          <  2:253203‑M1/143‑6 (MQ=255)     ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATATTATTTTCGCCACATCATAATCGTGGGCTTGCTGAAGAATAATTGACATGATATTATTAATTCCGCTGCCTTTGGTAAAGGAAAGTGCTAAataataatc                                                                                                                                      >  2:505160‑M1/1‑134 (MQ=255)           attaggaTTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                <  2:485887‑M1/140‑16 (MQ=255)           ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                >  1:707561‑M1/1‑128 (MQ=255)           ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAAAATAATTGAAATGATATTATTAATTCCACTGCCTTAGATAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                >  2:343658‑M1/1‑128 (MQ=255)                gATTTCCTTAACTGATTTTAATTACAAACAGGATATTTTCGCCAAATCATGATTCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaat                                                                                                                           >  1:732477‑M1/1‑123 (MQ=255)                 aTTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCTACATCATAATCCTGGGCTTGATGAAGAATAATTGAAATGATATTATTAATTCAATTGACTTTGGTAGAGGAAAGTGATAAataataataaattgttaaatt                                                                                                                          >  2:202458‑M1/1‑122 (MQ=255)                      cTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGCTACTACTACTTCCACTGACTTTGGTAGAGGAAAGTGCTAAatcataatcacttgttcaatcattgt                                                                                                                     >  2:183087‑M1/1‑117 (MQ=255)                      cTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCTCTGCCTTTGGTAGCGGAAAGTGCTAAataataatcacttgttaaattattgt                                                                                                                     >  1:305023‑M1/1‑117 (MQ=255)                      cTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatttt                                                                                                                     >  1:696167‑M1/1‑117 (MQ=255)                          aCTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcat                                                                                                                 <  1:730243‑M1/143‑31 (MQ=255)                              cTTCTCCTCCCCATCATGTTATTTTCGCCACATCATAATCCTAGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttca                                                                                                             <  1:7839‑M1/143‑35 (MQ=255)                              cTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGCGCTTGCTGAAGAATAATTAAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttca                                                                                                             <  2:49026‑M1/143‑35 (MQ=255)                                tctcCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcact                                                                                                           <  1:575044‑M1/143‑37 (MQ=255)                                 ctcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcacta                                                                                                          <  2:36515‑M1/143‑38 (MQ=255)                                   cctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAAGTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataaacaatcgttaaattattgcacacttaactact                                                                                                        >  2:542303‑M1/1‑104 (MQ=255)                                       tgcatcatgtTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                    <  2:107454‑M1/141‑44 (MQ=255)                                         catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTACCTGTGATAGAGGTAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaact                                                                                                  >  1:338227‑M1/1‑98 (MQ=255)                                            catGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattactgtgcatttcaatactagaaccgta                                                                                               >  2:475028‑M1/1‑95 (MQ=255)                                              tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                             <  2:231346‑M1/143‑51 (MQ=255)                                                  aTTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcaga                                                                                         >  2:633596‑M1/1‑89 (MQ=255)                                                   ttttCGCCACATCATAATCCTGGGCTGGCTGAAGAATAATTGAAATGATATTATTGATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaa                                                                                        <  2:110278‑M1/143‑56 (MQ=255)                                                     ttCGCCACATCATAATGCTGGGCTTGCTGAAGAATAATTGAAAGGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                      <  2:542552‑M1/143‑58 (MQ=255)                                                     ttCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                      >  2:375181‑M1/1‑86 (MQ=255)                                                     ttCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                      <  1:678393‑M1/143‑58 (MQ=255)                                                         ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaattagaaaagata                                                                                  >  2:413852‑M1/1‑82 (MQ=255)                                                         ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagata                                                                                  >  1:711881‑M1/1‑82 (MQ=255)                                                         ccACATCATAAGCCTGGGCTGGCTGAAGGATAATTGAAATGAAATTAGTAATCCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagata                                                                                  <  1:306281‑M1/143‑62 (MQ=255)                                                          cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatag                                                                                 >  1:510360‑M1/1‑81 (MQ=255)                                                           acaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagataga                                                                                >  1:428205‑M1/1‑80 (MQ=255)                                                                 tAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgct                                                                          >  1:274365‑M1/1‑74 (MQ=255)                                                                      cTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttatcc                                                                     >  1:224177‑M1/1‑69 (MQ=255)                                                                           cTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatct                                                                >  2:423158‑M1/1‑64 (MQ=255)                                                                                 gaagaaTAATTGAAATGATATTATTAATTCCACCGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                          >  2:89685‑M1/1‑58 (MQ=255)                                                                                   agaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttga                                                        <  1:353071‑M1/143‑88 (MQ=255)                                                                                      ataatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattg                                                     <  2:466033‑M1/143‑91 (MQ=255)                                                                                        aatTGAAATGATATTATTAATTCCACTGCCTGTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaa                                                   <  1:157482‑M1/143‑93 (MQ=255)                                                                                              aaTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacgtgcttagccaatctctatttgattgaattgaaa                                             <  2:626385‑M1/143‑99 (MQ=255)                                                                                                    attattAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcacttgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgacttgaaagatgtt                                       >  1:468535‑M1/1‑39 (MQ=255)                                                                                                    attattAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtt                                       <  1:265522‑M1/143‑105 (MQ=255)                                                                                                     ttattaATTCCACTGCCGTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                      <  2:168397‑M1/143‑106 (MQ=255)                                                                                                     ttattaAGTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                      <  1:317591‑M1/143‑106 (MQ=255)                                                                                                        tgaattCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgtt                                   >  1:538885‑M1/3‑35 (MQ=255)                                                                                                           aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtt                                       <  2:360093‑M1/136‑105 (MQ=255)                                                                                                           aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtt                                       >  1:360093‑M1/1‑32 (MQ=255)                                                                                                               cACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcat                            <  1:633596‑M1/143‑116 (MQ=255)                                                                                                                  tGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatgga                         >  1:573182‑M1/1‑25 (MQ=255)                                                                                                                     cTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgc                      >  1:18015‑M1/1‑22 (MQ=255)                                                                                                                       ttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                    >  1:112113‑M1/1‑20 (MQ=255)                                                                                                                          gTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagct                 <  1:573348‑M1/143‑127 (MQ=255)                                                                                                                                gAAAGTGCTAAataataatcaattgttaaagtattgtgcatttcactactggaactgtaatcagaaaagatcgacatgcttagccaatcgctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagat           >  2:431889‑M1/1‑11 (MQ=255)                                                                                                                                  aaGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattc         <  1:899‑M1/143‑135 (MQ=255)                                                                                                                                   aGTGCTAAataagaatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct        <  2:198550‑M1/143‑136 (MQ=255)                                                                                                                                      gCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgat     <  2:558301‑M1/143‑139 (MQ=255)                                                                                                                                       cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgata    <  2:607248‑M1/143‑140 (MQ=255)                                                                                                                                        tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatggttgttaaggcatggatgcaagctatagattctgatac   >  1:47240‑M1/1‑3 (MQ=255)                                                                                                                                        tAAataataatcaattgttaaattattgtgcatttcactactgaaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatac   >  2:628516‑M1/1‑3 (MQ=255)                                                                                                                                        tAAataataatcaatggttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggctgcaagctatagattctgatac   >  2:617517‑M1/1‑3 (MQ=255)                                                                                                                                         aaataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacg  <  1:510513‑M1/143‑142 (MQ=255)                                                                                                                                          |                                                                                                                                              ACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT  >  NC_000913/1299361‑1299639

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: ‑