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	47 [0]	[1] 48	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)	45 (1.030)	35/276	0.2	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

AACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGG  >  NC_000913/1300559‑1300839                                                                                                                                            |                                                                                                                                              gcgagctggtcataagggttgccgtaactgcttctcctcaccatcatgttattttcgccacatcataagcctgggcttgctgaagaataagtgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                            <  2:54330‑M2/4‑1 (MQ=255)    agttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataa                                                                                                                                         <  1:771632‑M2/7‑1 (MQ=255)      ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgatgaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATc                                                                                                                                       >  2:634193‑M2/135‑143 (MQ=255)          ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                   <  1:217502‑M2/13‑1 (MQ=255)          ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                   <  2:446824‑M2/13‑1 (MQ=255)          ttataaggatttcctgaactgcttcgccgcaccatcatgttattttcgccacatcataagcctgggcttgctgaagaataattgaaatgatattagtaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                   <  1:68654‑M2/13‑1 (MQ=255)                 gatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAat                                                                                                                            >  1:327955‑M2/124‑143 (MQ=255)                      ccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtg                                                                                                                       <  2:76790‑M2/25‑1 (MQ=255)                        ttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgtg                                                                                                                     >  2:140877‑M2/117‑143 (MQ=255)                             tgcttctcctcaccatcatggtattttcgccacatcataatcctgggcttgctgaagaataattgaaaggatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAttt                                                                                                                <  2:128027‑M2/32‑1 (MQ=255)                               cttctcctcaccgtcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                              <  2:218275‑M2/34‑1 (MQ=255)                               cttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                              <  1:338400‑M2/34‑1 (MQ=255)                                ttctcctgaccatcatgttgttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCac                                                                                                             <  2:562250‑M2/35‑1 (MQ=255)                                ttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCac                                                                                                             <  1:763700‑M2/35‑1 (MQ=255)                                  ctcctctccatgtggtaactttctccagatcataattctgggcttgctgaagaagaattgaaatgatattattaatttcactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                           <  2:507627‑M2/37‑1 (MQ=255)                                  ctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                           <  2:566205‑M2/37‑1 (MQ=255)                                   tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgacatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactac                                                                                                          >  1:704613‑M2/106‑143 (MQ=255)                                    cctcgccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactact                                                                                                         <  2:342648‑M2/39‑1 (MQ=255)                                        accatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                     >  2:743769‑M2/101‑143 (MQ=255)                                          cattacggtactttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgtctttggtagaggaaagtgctaaATAATAATCAATTGTTAAAATATTGTGCATTTCACTACTGGAACt                                                                                                   <  2:183359‑M2/45‑1 (MQ=255)                                          catcgtgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACt                                                                                                   <  1:412485‑M2/45‑1 (MQ=255)                                                 ttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatcttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTACATTATAGTGCATTTCACTACTGGACCTGTAATCa                                                                                            >  2:443425‑M2/92‑143 (MQ=255)                                                      ttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccattgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaaa                                                                                       >  1:495662‑M2/87‑143 (MQ=255)                                                          ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaatacaactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGAAACTGTAATCAGAAGAGATa                                                                                   >  1:646606‑M2/83‑143 (MQ=255)                                                           cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAg                                                                                  <  1:230769‑M2/62‑1 (MQ=255)                                                           cacatcataatcctgggcttgctcaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAg                                                                                  <  1:67120‑M2/62‑1 (MQ=255)                                                            acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGa                                                                                 >  1:254049‑M2/81‑143 (MQ=255)                                                                      cctgggcttgctgaagagtaattgaaatgatattattgattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                       <  2:643643‑M2/73‑1 (MQ=255)                                                                               gctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTa                                                              <  2:100187‑M2/82‑1 (MQ=255)                                                                                 tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                            >  2:634433‑M2/60‑143 (MQ=255)                                                                                    agaataattgaaatgatattagtaattccactgtctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                         <  2:137966‑M2/87‑1 (MQ=255)                                                                                     gaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgat                                                        <  1:552071‑M2/88‑1 (MQ=255)                                                                                      aataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                       <  1:427685‑M2/89‑1 (MQ=255)                                                                                               aatgatattattaagtccactgccgttggtagaggaaagtgcttgTTTATAATCAATTGTTAAATTATGGTGCATTTCACTACTGGAACTGTAATCAGAAAAGAGAGACATGCTTAGCCAATCTCTATTTGATTGAATTGaaa                                              <  1:532310‑M2/98‑1 (MQ=255)                                                                                                            attccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAACGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAg                                 >  2:127646‑M2/33‑143 (MQ=255)                                                                                                                 actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                            <  1:594506‑M2/116‑1 (MQ=255)                                                                                                                 actgcatttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTTCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                            >  1:662880‑M2/28‑143 (MQ=255)                                                                                                                         tggtagaggaaagtgctaaATAATAATCAATTGTTAAATAATGGTGCATTACACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATATGATAGAATAGAAAGAAGTTAGATAAGCCACGAATGCAAg                    >  2:546386‑M2/20‑143 (MQ=255)                                                                                                                          gttagaggaaagttataaATAATAATCAATTGATAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAACATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGc                   <  2:719798‑M2/125‑1 (MQ=255)                                                                                                                            tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCta                 >  1:540968‑M2/17‑143 (MQ=255)                                                                                                                              gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata               <  1:10606‑M2/129‑1 (MQ=255)                                                                                                                              gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata               >  1:669861‑M2/15‑143 (MQ=255)                                                                                                                              gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata               >  1:686019‑M2/15‑143 (MQ=255)                                                                                                                               aggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAg              >  1:366773‑M2/14‑143 (MQ=255)                                                                                                                               aggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAGGCTTAGCCAATCCTAATATTATTTATTTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAg              >  1:743508‑M2/14‑143 (MQ=255)                                                                                                                                  taagttcaaaaTAATCATCAATTGTTAAATTATTGTGTATTTCACTACCTGAACTGTATTCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAtt           <  2:382477/135‑1 (MQ=255)                                                                                                                                          aaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg   >  2:100793‑M2/3‑143 (MQ=255)                                                                                                                                           aATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACgg  <  2:254049‑M2/142‑1 (MQ=255)                                                                                                                                            |                                                                                                                                              AACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGG  >  NC_000913/1300559‑1300839

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: ‑