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	1300697–1299500	2–1199	46 [0]	[0] 46	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)	44 (1.010)	39/276	0.1	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

AATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTC  >  NC_000913/1299357‑1299638                                                                                                                                              |                                                                                                                                             aaTTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAa                                                                                                                                             <  1:549579‑M1/143‑2 (MQ=255)       agttagtcATAAGCATTTCCTTAGCTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataa                                                                                                                                       <  1:22877‑M1/143‑8 (MQ=255)         ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCCTAATCCTGGGCTTGCTGACGAATAATTGAACTGATATTATTAATTACACTCCCTCTGGTAGAAGAAAGTGCTAAataataatc                                                                                                                                     >  2:89687‑M1/1‑134 (MQ=255)         ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                     >  1:621109‑M1/1‑134 (MQ=255)               ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                               >  1:516763‑M1/1‑128 (MQ=255)                taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgtt                                                                                                                              >  1:702938‑M1/1‑127 (MQ=255)                   ggATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaa                                                                                                                           >  2:189131‑M1/1‑124 (MQ=255)                    gATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCCTAATCCTGGGCTTGCTGACGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTATAGGACAGTGCTAAataataatcaattgttaaat                                                                                                                          >  2:587571‑M1/1‑123 (MQ=255)                        tCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                      <  1:394923‑M1/143‑25 (MQ=255)                          cTTAACTGGTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgt                                                                                                                    <  2:250222‑M1/143‑27 (MQ=255)                                     ctcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcacta                                                                                                         <  1:734359‑M1/143‑38 (MQ=255)                                        ctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                      >  2:311659‑M1/1‑103 (MQ=255)                                         tcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcacttgttaaattattgtgcatttcactactgg                                                                                                     >  2:250722‑M1/1‑102 (MQ=255)                                            ccctcatgttATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaac                                                                                                  <  1:59978‑M1/140‑45 (MQ=255)                                            ccATCATGTTATTTTCGCCACATCATAATCCTTGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTTCTAAataataatcaattgttaaattattgtgcatttcactactggaac                                                                                                  <  2:716987‑M1/143‑45 (MQ=255)                                            ccATCATGTTATTTTCGCCACATCATAATCCTGTGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaac                                                                                                  <  1:625546‑M1/143‑45 (MQ=255)                                             catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTCTGGTAGAGGAAAGTGCTAAataataatcaattgttcaaatattgcgtatcacactactgaaatt                                                                                                 >  2:310294‑M1/1‑98 (MQ=255)                                               tcatGGTATTTTCGCCACATGATAATCCTGGGCTTGCTGAAGAATAAGTGAAATGATATTATTAATTCCACTGCCGTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgt                                                                                               <  2:401044‑M1/143‑48 (MQ=255)                                                 ttgTTATTTTCGCAACTTCATAATCCTGTGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaa                                                                                             <  2:636037‑M1/142‑50 (MQ=255)                                                  tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtact                                                                                            >  1:411574‑M1/1‑93 (MQ=255)                                                    ttATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatca                                                                                          >  1:638296‑M1/1‑91 (MQ=255)                                                        gttcGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaa                                                                                      <  1:772420‑M1/142‑57 (MQ=255)                                                         ttCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                     <  2:179369‑M1/143‑58 (MQ=255)                                                                    atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcgctactggaactgtaatcagaaaagatagacatgc                                                                          >  1:238953‑M1/1‑75 (MQ=255)                                                                        tCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTATAGAAGAAGAAAGTGATAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttag                                                                      >  1:645672‑M1/1‑71 (MQ=255)                                                                              gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatc                                                                >  1:738819‑M1/1‑65 (MQ=255)                                                                                ttGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctc                                                              >  1:120290‑M1/1‑63 (MQ=255)                                                                                  gCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctcta                                                            <  1:474592‑M1/143‑83 (MQ=255)                                                                                  gCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctcta                                                            <  1:209138‑M1/143‑83 (MQ=255)                                                                                     gaagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                         >  1:432376‑M1/1‑58 (MQ=255)                                                                                        gaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgat                                                      <  1:267154‑M1/143‑89 (MQ=255)                                                                                         aataatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgatt                                                     <  1:347397‑M1/143‑90 (MQ=255)                                                                                         aataatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgatt                                                     >  1:93892‑M1/1‑54 (MQ=255)                                                                                         aataatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgatc                                                     >  1:778528‑M1/1‑54 (MQ=255)                                                                                                gAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattga                                              >  1:187379‑M1/1‑47 (MQ=255)                                                                                                 caatagtatgatcaattcCACTGCCTTTGCTAGAGGAAAGTTCTAAataataatcaattgttaaattattgtgcattttactactctaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaa                                             <  2:232060‑M1/137‑98 (MQ=255)                                                                                                     gATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                         >  2:442268‑M1/1‑42 (MQ=255)                                                                                                      atatTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatc                                        >  1:289798‑M1/1‑41 (MQ=255)                                                                                                              aaTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaa                                <  1:189131‑M1/143‑111 (MQ=255)                                                                                                               aTTACACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaagtgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaag                               <  2:768606‑M1/143‑112 (MQ=255)                                                                                                                   cACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcat                           <  2:621109‑M1/143‑116 (MQ=255)                                                                                                                      tGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaacgatgtttgttaaggcatgga                        >  1:725650‑M1/1‑25 (MQ=255)                                                                                                                                    gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagat          >  2:96978‑M1/1‑11 (MQ=255)                                                                                                                                         tGCTAAataataatcaattgttaaatgattgtgcatttcactactggaacggtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctga     <  1:89042‑M1/143‑138 (MQ=255)                                                                                                                                           cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgata   <  2:187379‑M1/143‑140 (MQ=255)                                                                                                                                            tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatac  >  1:773675‑M1/1‑3 (MQ=255)                                                                                                                                              |                                                                                                                                             AATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTC  >  NC_000913/1299357‑1299638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑