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	54 [0]	[1] 55	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)	51 (1.100)	45/274	0.1	99.0%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	1 (0.020)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

GATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT  >  NC_000913/1300556‑1300840                                                                                                                                               |                                                                                                                                                aattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaa                                                                                                                                                 <  1:606163‑M2/1‑1 (MQ=255)    tactgttagttatacggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                              <  2:238202‑M2/4‑1 (MQ=255)      cGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAaataatc                                                                                                                                            >  1:527062/1‑142 (MQ=14)          tagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCa                                                                                                                                       <  1:498565‑M2/10‑1 (MQ=255)           agttataaggatttccttaactgcttctcctcaccatcctgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCaa                                                                                                                                      <  1:72909‑M2/11‑1 (MQ=255)           agttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagcggaaagtgctcaATAATA‑ATcac                                                                                                                                      >  1:695488‑M2/133‑142 (MQ=255)             ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAAtt                                                                                                                                    <  2:94268‑M2/13‑1 (MQ=255)              tataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTg                                                                                                                                   <  2:229312‑M2/14‑1 (MQ=255)               ataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgcagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGt                                                                                                                                  >  2:189926‑M2/129‑143 (MQ=255)                taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGtt                                                                                                                                 >  1:484577‑M2/128‑143 (MQ=255)                   ggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTaaa                                                                                                                              >  1:438753‑M2/125‑143 (MQ=255)                     atttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAatt                                                                                                                            >  2:497832‑M2/123‑143 (MQ=255)                      tttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAatta                                                                                                                           >  2:435534‑M2/122‑143 (MQ=255)                        tccttacctgcttctcctccccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgtctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAattatt                                                                                                                         <  2:504238‑M2/24‑1 (MQ=255)                          cttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATtgt                                                                                                                       >  1:761772‑M2/118‑143 (MQ=255)                                tgcttctcctcaccatcatgttattttcgccacatcatactcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATCGtacaatg                                                                                                                 >  2:128199‑M2/112‑140 (MQ=255)                                      gcctcaccatcatgttattttcgcgacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagttctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCactac                                                                                                           <  2:155567‑M2/38‑1 (MQ=255)                                        ctcaccatcatgttattttcgccaaatcaaaatcctggtcgtgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAACTTATTGTGCATTTCACTACTg                                                                                                         >  2:572170‑M2/104‑143 (MQ=255)                                         tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTgg                                                                                                        <  2:657369‑M2/41‑1 (MQ=255)                                             catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACAGGAACt                                                                                                    >  2:638200‑M2/99‑143 (MQ=255)                                               taatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGCACTGt                                                                                                  >  2:351421‑M2/97‑143 (MQ=255)                                                    ttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                             >  1:70982‑M2/92‑143 (MQ=255)                                                       ttttcgccacatcataatcctgggcttgctgaagaataatttaaatgatattattaattccactgcctttggtagaggaaagtgctaaATCATA‑ATTATCCGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                          >  2:792809‑M2/89‑143 (MQ=255)                                                       ttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                          <  2:470263‑M2/55‑1 (MQ=255)                                                       ttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgccaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                          <  1:496174‑M2/55‑1 (MQ=255)                                                          tcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAg                                                                                       >  2:69642‑M2/86‑143 (MQ=255)                                                           cgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGa                                                                                      <  2:313205‑M2/59‑1 (MQ=255)                                                             ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                    <  2:112156‑M2/61‑1 (MQ=255)                                                             ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                    <  2:484577‑M2/61‑1 (MQ=255)                                                              cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAg                                                                                   >  1:805266‑M2/82‑143 (MQ=255)                                                                    ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAATATAGACATGc                                                                             >  2:107623‑M2/76‑143 (MQ=255)                                                                    ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGc                                                                             <  2:647366‑M2/68‑1 (MQ=255)                                                                        tcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAg                                                                         <  1:757143‑M2/72‑1 (MQ=255)                                                                                   ctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAt                                                              <  2:692386‑M2/83‑1 (MQ=255)                                                                                   cggaagaataattgaactggtattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAt                                                              <  1:1222‑M2/83‑1 (MQ=255)                                                                                    tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                             >  1:714919‑M2/60‑143 (MQ=255)                                                                                      aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttg                                                           >  1:447903‑M2/58‑143 (MQ=255)                                                                                      aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttg                                                           >  1:750670‑M2/58‑143 (MQ=255)                                                                                       agaataattgaaacgatattatcaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                          <  2:695488‑M2/87‑1 (MQ=255)                                                                                       agaagaattggaatgatattattaattccactgcgtttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCCATttga                                                          <  2:575090‑M2/87‑1 (MQ=255)                                                                                         aataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                        <  2:659639‑M2/89‑1 (MQ=255)                                                                                           taattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgattga                                                      >  1:51596‑M2/53‑143 (MQ=255)                                                                                            aattgaaatgatattattaattccactgcctttggtagaggaaagtgctccA‑AGTATATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                     <  1:195982‑M2/92‑1 (MQ=255)                                                                                              ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaatt                                                   <  2:246805‑M2/94‑1 (MQ=255)                                                                                                 agatgatattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGAttgaattgaa                                                <  2:110814‑M2/97‑1 (MQ=255)                                                                                                      atattattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGATATGCTTAGCCAATCTCTATTTGATTGAATTGAAagagg                                           >  2:193108‑M2/42‑141 (MQ=255)                                                                                                        attattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                         <  2:240610‑M2/104‑1 (MQ=255)                                                                                                          tattaattccactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttg                                       >  1:639052‑M2/38‑143 (MQ=255)                                                                                                                   cactgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                              >  2:771338‑M2/29‑143 (MQ=255)                                                                                                                    actgcctttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                             <  2:805266‑M2/116‑1 (MQ=255)                                                                                                                           ttggtagaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                      <  1:109984‑M2/123‑1 (MQ=255)                                                                                                                                agaggaaagtgctaaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                 >  2:81391‑M2/16‑143 (MQ=255)                                                                                                                                             aaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg    <  1:69642‑M2/141‑1 (MQ=255)                                                                                                                                             aaATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGGAATCAGAAAAGAGAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg    <  1:435534‑M2/141‑1 (MQ=255)                                                                                                                                               ataata‑atCAATTGTTAAATTATTGTGCATTGCACTACTGGAACTGGAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTTAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt  <  1:270563/143‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                GATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATA‑ATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT  >  NC_000913/1300556‑1300840

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: ‑