Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_KO_pgi	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_3_KO_pgi	1299499–1300695	1300697	3–1199	57 [0]	[0] 57	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_3_KO_pgi	= 1299498	0 (0.000)	56 (1.130)	46/278	0.1	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_KO_pgi	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

TGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_KO_pgi/1300552‑1300843                                                                                                                                                   |                                                                                                                                                   ctcaaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaata                                                                                                                                                  >  2:283749‑M2/147‑149 (MQ=255)  tcaaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                                 >  1:123776‑M2/146‑149 (MQ=255)    aaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataata                                                                                                                                               <  1:703950‑M2/6‑1 (MQ=255)     aattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgatgaaggataggggaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataa                                                                                                                                              >  1:433813‑M2/143‑149 (MQ=255)          cagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAAt                                                                                                                                        >  2:905468‑M2/138‑149 (MQ=255)             ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCATTTGt                                                                                                                                     >  1:135136‑M2/135‑149 (MQ=255)                     aaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgatcaATAATAA‑CCACtttttaatcaat                                                                                                                             >  2:398966‑M2/127‑144 (MQ=255)                         atttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaatgattgaaatgatattattaattccactgcctttggtagaggaaagtactacAAAATAA‑TCAACTGTTAAATTATtgtg                                                                                                                         >  2:657965‑M2/123‑149 (MQ=255)                              cttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCAttt                                                                                                                    >  1:853542‑M2/118‑149 (MQ=255)                                   ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagagtaaagtgctaaATAATAA‑TCAATTTTTAATTTATTGTACATTTCccta                                                                                                               >  2:426786‑M2/113‑149 (MQ=255)                                   ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCacta                                                                                                               <  1:738509‑M2/37‑1 (MQ=255)                                     gcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCactact                                                                                                             <  1:283749‑M2/39‑1 (MQ=255)                                       ttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtaggggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCAATACTgg                                                                                                           >  1:597381‑M2/109‑149 (MQ=255)                                       ttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTgg                                                                                                           >  1:515685‑M2/109‑149 (MQ=255)                                          tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAAc                                                                                                        <  2:123776‑M2/44‑1 (MQ=255)                                            ctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGaacag                                                                                                      >  1:184359‑M2/104‑147 (MQ=255)                                             tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGt                                                                                                     <  2:322775‑M2/47‑1 (MQ=255)                                               accatcctgttattttcgccacatcataaccctgggctttctgaagaataattgaaatgatattattaattccactgccttttgtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTaa                                                                                                   <  2:480982‑M2/49‑1 (MQ=255)                                               accatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTTTTCATTTCATTACTGGAACTTTaa                                                                                                   >  1:32952‑M2/101‑149 (MQ=255)                                                      tgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTATTCAATTATTGTGCATTTCACTACTGGAACTGTAATCAGgaa                                                                                            >  1:165428‑M2/94‑149 (MQ=255)                                                       gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaaa                                                                                           <  1:272570‑M2/57‑1 (MQ=255)                                                       gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACGGCTTGAACTGTAATCAGaaaa                                                                                           <  2:878697‑M2/57‑1 (MQ=255)                                                        ttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAg                                                                                          >  2:573221‑M2/92‑149 (MQ=255)                                                             ttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGa                                                                                     <  1:759506‑M2/63‑1 (MQ=255)                                                                        ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGcc                                                                          >  1:140616‑M2/76‑149 (MQ=255)                                                                            tcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAtc                                                                      >  2:179575‑M2/72‑149 (MQ=255)                                                                               ttggcttgctgaagaattagtgaaattatattattaattccactgcctttggtagaggaaattgctaaTTTATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGCCTTTCTTAGCCAATctct                                                                   <  2:335002‑M2/81‑1 (MQ=255)                                                                               tgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATctct                                                                   <  2:335004‑M2/81‑1 (MQ=255)                                                                                        tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTa                                                                             >  2:716206‑M2/60‑130 (MQ=255)                                                                                        tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTa                                                                             <  1:716327‑M2/71‑1 (MQ=255)                                                                                        tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTa                                                                             <  1:716206‑M2/71‑1 (MQ=255)                                                                                        tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTa                                                                             >  2:716327‑M2/60‑130 (MQ=255)                                                                                        tgaagaataattgaaatgatattattaattccactgcctttgagagaggaaagtgctgcAAGAGAA‑TAAATTGTTAAATCATTATGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATATCTATttgcttg                                                          >  2:871641‑M2/60‑149 (MQ=255)                                                                                                aattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGaaa                                                  <  2:433813‑M2/98‑1 (MQ=255)                                                                                                  ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                           >  1:745283‑M2/50‑122 (MQ=255)                                                                                                  ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                           <  2:745283‑M2/73‑1 (MQ=255)                                                                                                      aatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGAAATGCTTAGCCAATCTCTATTTTATTGAATAGAAAGAtgtt                                            >  2:220363‑M2/46‑149 (MQ=255)                                                                                                       atgatattattaattccactggcgtttggagaggaaagtgtgaaATAATAA‑TCAATTTTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                           <  2:368910‑M2/105‑1 (MQ=255)                                                                                                           tattattaattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGTTTAGCCAATCTCTATTTGATTGAATTGAAAGGTGTTTGTTa                                       >  2:765936‑M2/41‑149 (MQ=255)                                                                                                                  aattccactgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCACTATAAACGCCGGTTAATTGAAAGATGTTTGTTAAGGCATg                                <  1:670435‑M2/116‑1 (MQ=255)                                                                                                                     tccactgcctttggtagaggaaagtgctaaATAATAA‑TCAAGTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt                             <  1:271114‑M2/119‑1 (MQ=255)                                                                                                                      cccctggctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGCAACTGTAATCAGAAAAGATAGACAGGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATg                            <  1:372472‑M2/120‑1 (MQ=255)                                                                                                                        actgcctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAAATGTTTGTTAAGCCATGAATGCa                          >  2:15171‑M2/28‑149 (MQ=255)                                                                                                                        actgcctttggtagaggaaagtgataaATAATGA‑TCAATTGTGAACTTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATgcc                          >  1:715291‑M2/28‑148 (MQ=255)                                                                                                                            cctttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCt                      >  2:390649‑M2/24‑149 (MQ=255)                                                                                                                              tttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    <  1:482447‑M2/128‑1 (MQ=255)                                                                                                                              tttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    <  1:179575‑M2/128‑1 (MQ=255)                                                                                                                              tttggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGGGCATTTCACTACTGGAACTGTAATCCGAATAGATAGACATGCTTAGCCAATCACTATTTGATTAAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    >  2:512425‑M2/22‑149 (MQ=255)                                                                                                                              tttggtagaggaaagtactaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    >  1:788678‑M2/22‑149 (MQ=255)                                                                                                                               ttggtagaggaaagtgctaaATACTAACGCCATTG‑TGTGTTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGACATGGATGAAAGCtata                   >  2:420187‑M2/21‑149 (MQ=255)                                                                                                                                 ggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGa                 >  1:75086‑M2/19‑149 (MQ=255)                                                                                                                                 ggtagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGa                 <  1:190649‑M2/131‑1 (MQ=255)                                                                                                                                   tagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                                  >  2:417043‑M2/17‑66 (MQ=255)                                                                                                                                   tagaggaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                                  <  1:417043‑M2/50‑1 (MQ=255)                                                                                                                                        gaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGAt          >  1:145946‑M2/12‑149 (MQ=255)                                                                                                                                        gaaagtgctaaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAAGTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGAt          >  1:344610‑M2/12‑149 (MQ=255)                                                                                                                                                taaATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCaa  <  2:593979‑M2/146‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                   TGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAA‑TCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_KO_pgi/1300552‑1300843

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑