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	60 [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 (0.850)	46/274	0.4	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

CCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACG  >  NC_000913/1300563‑1300838                                                                                                                                        |                                                                                                                                              gttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagcataattgaaatgatattattaattccactgcctttggtagaggaaagtgcgaaataataat                                                                                                                                        >  2:449877‑M2/136‑143 (MQ=255)    tgttataaggatttccttaactgcttctcctcaccgtcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCaa                                                                                                                                     <  2:616970‑M2/11‑1 (MQ=255)      ttataaggctttccttaactgcttctcctcaccatcatgttattttcgccacatcctaatcctggccttcctgacgaataattgaaatgatattattaattcccctgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                   >  2:461179‑M2/131‑143 (MQ=255)      ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                   <  2:1062435‑M2/13‑1 (MQ=255)        ataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATtgc                                                                                                                                 >  2:650968‑M2/129‑142 (MQ=255)         taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGtt                                                                                                                                >  1:307445‑M2/128‑143 (MQ=255)            ggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttgggaaggtgttttggtagATAATAATCAATTGTTaaa                                                                                                                             >  1:918131‑M2/125‑143 (MQ=255)              atttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctcggcttgctgcagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAACAATCAATTCTTAaatc                                                                                                                           >  2:963804‑M2/123‑142 (MQ=255)                 tccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                        <  1:228373‑M2/24‑1 (MQ=255)                 tccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                        <  1:247760‑M2/24‑1 (MQ=255)                    ttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaataatattattaattccactacctttgatatatgaaaatgctaaATAATAATCAATAGTTAAATTATtttg                                                                                                                     >  2:74221‑M2/117‑143 (MQ=255)                           cttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                              <  1:123184‑M2/34‑1 (MQ=255)                           cttctcctcaccatcatgttattttcgccacagcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                              <  1:491517‑M2/34‑1 (MQ=255)                                cctcaccatcatgttattttcgccgcatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactact                                                                                                         >  1:873565‑M2/105‑143 (MQ=255)                                 ctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTg                                                                                                        >  1:1057979‑M2/104‑143 (MQ=255)                                      catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACt                                                                                                   >  2:202534‑M2/99‑143 (MQ=255)                                         catgttattttcgccacatcatactcctgggcttgctgaagaataattgaaatgatattatcaattccactgcctttggtagaggaaagtgctaaAATATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTa                                                                                                <  1:840298‑M2/48‑1 (MQ=255)                                           tgttatttgcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑At                                                                                             <  2:157593‑M2/50‑1 (MQ=255)                                           tgttattgtcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑At                                                                                             <  1:176315‑M2/50‑1 (MQ=255)                                            gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATc                                                                                            >  1:84577‑M2/93‑143 (MQ=255)                                            gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATc                                                                                            >  1:889890‑M2/93‑143 (MQ=255)                                            gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattataaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATc                                                                                            >  1:79929‑M2/93‑143 (MQ=255)                                             ttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCa                                                                                           >  1:1095125‑M2/92‑143 (MQ=255)                                                ttgtcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagacgaaagtgctaaATAATAATCAATTGTTAAATTATTGATCATTTCACTACTAGAACTATA‑ATCAGaa                                                                                        >  2:1135261‑M2/89‑143 (MQ=255)                                                 tttcgtcacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGaaa                                                                                       <  2:1031362‑M2/56‑1 (MQ=255)                                                       cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAg                                                                                 <  1:477655‑M2/62‑1 (MQ=255)                                                       cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACCACTGAAACTGTA‑ATCAGAAAAGATAg                                                                                 >  2:445200‑M2/82‑143 (MQ=255)                                                        acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGa                                                                                >  1:233415‑M2/81‑143 (MQ=255)                                                        acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGa                                                                                <  1:682467‑M2/63‑1 (MQ=255)                                                          atcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACa                                                                              <  1:983920‑M2/65‑1 (MQ=255)                                                            cataatcctgcgcttgcgtaagaataattgaaattatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATg                                                                            <  1:189841‑M2/67‑1 (MQ=255)                                                             ataatcctgggcttgctggagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGc                                                                           <  1:218339‑M2/68‑1 (MQ=255)                                                                 tcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAg                                                                       >  2:741333‑M2/72‑143 (MQ=255)                                                                      ggcttgcggaagaataattgaaatgagattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAAt                                                                  <  2:8943‑M2/77‑1 (MQ=255)                                                                             tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTATA‑ATCAGAAAAGATAGACATGCATAGCCACTCTCGAtt                                                           >  2:911517‑M2/60‑143 (MQ=255)                                                                              gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                          <  1:837090‑M2/85‑1 (MQ=255)                                                                              gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                          <  1:193907‑M2/85‑1 (MQ=255)                                                                                agaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                        <  2:647208‑M2/87‑1 (MQ=255)                                                                                agaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                        <  2:119782‑M2/87‑1 (MQ=255)                                                                                  aataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                      >  2:590232‑M2/55‑143 (MQ=255)                                                                                     aattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                   <  1:1137836‑M2/92‑1 (MQ=255)                                                                                      actcatgagatattattagtgccaccgcctctggtagaggaaagtgctacATAATAATCAATTGTCAAATTATTGTGCACTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCGTAGCCAATCTCTATTTGattgaat                                                  <  1:874944‑M2/93‑1 (MQ=255)                                                                                          aaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGAgtgacttgaa                                              >  2:1076743‑M2/47‑143 (MQ=255)                                                                                           aatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGaaa                                             <  1:217266‑M2/98‑1 (MQ=255)                                                                                               atattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtg                                         >  2:541039‑M2/42‑143 (MQ=255)                                                                                                 attattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGCTAGACATGCTTAGCCAATATCTATTTGATTGAACTGAAAGAtgtt                                       >  1:384529‑M2/40‑143 (MQ=255)                                                                                                 attattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                       >  1:384534‑M2/40‑143 (MQ=255)                                                                                                 attattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                       >  1:384535‑M2/40‑143 (MQ=255)                                                                                                 attagtaattccacgggctttggtagaggaaagtgctaaATAATAATCAAGTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                       <  2:1119257‑M2/104‑1 (MQ=255)                                                                                                       aattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTaa                                 <  2:1183593‑M2/110‑1 (MQ=255)                                                                                                        attccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTACATC‑GTACTAAGAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAg                                >  1:547145‑M2/33‑143 (MQ=255)                                                                                                         ttccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAgg                               >  1:189734‑M2/32‑143 (MQ=255)                                                                                                            cactgcctttggtcgaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                            <  2:1095125‑M2/115‑1 (MQ=255)                                                                                                            cactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                            >  1:412047‑M2/29‑143 (MQ=255)                                                                                                                   tttggtagaggaaagtgctacATAATAATCAATTGTTAAATTATTGTGCATTTAACAACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCa                     >  1:345402‑M2/22‑143 (MQ=255)                                                                                                                    ttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                    <  1:706152‑M2/123‑1 (MQ=255)                                                                                                                                    ctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATa    <  2:1057979‑M2/139‑1 (MQ=255)                                                                                                                                     taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAGTTGAAAGATGTGTGTTAAGGCATGGATGCAAGCTATAGATTCTGAtag   >  1:726923‑M2/4‑142 (MQ=255)                                                                                                                                      aaATAATAATCAATTGTTAAATTATTGTGCATTTCACCACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCGGTCGCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg  <  1:445200‑M2/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                              CCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTA‑ATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACG  >  NC_000913/1300563‑1300838

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: ‑