Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	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_pae_tpiA	1299499–1300697	1300697	1–1199	33 [0]	[0] 33	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_pae_tpiA	= 1299498	0 (0.000)	32 (1.130)	31/274	0.1	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_pae_tpiA	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

ATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTC  >  NC_000913_3_pae_tpiA/1300557‑1300841                                                                                                                                              |                                                                                                                                                attactgttaggtatatggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataat                                                                                                                                          <  2:49677‑M2/8‑1 (MQ=255)        ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGt                                                                                                                                   >  1:363098‑M2/135‑149 (MQ=255)        ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgacattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGt                                                                                                                                   >  1:404940‑M2/135‑149 (MQ=255)          agttataaggatttacttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgagcttgctgaagaataattttaatgatattattaattctactgcctttggtacaggaaattgctaaATAATACTCAATTGTTa                                                                                                                                 >  2:338576‑M2/133‑149 (MQ=255)            ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaaa                                                                                                                               <  2:408731‑M2/19‑1 (MQ=255)                          ttaactgcttctcctcaccatcatgttattttcgccacatcataatgctgggcttgctgaagaataagtgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATATCGAATTGTTGAATTATTGTGCattta                                                                                                                 >  1:465538‑M2/117‑148 (MQ=255)                              ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                             >  2:112517‑M2/113‑149 (MQ=255)                                gcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactact                                                                                                           >  2:165264‑M2/111‑149 (MQ=255)                                 cttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTg                                                                                                          <  2:473174‑M2/40‑1 (MQ=255)                                           ctatcatgttgttttcgtccaatcattatcctgggcttggtggataagaattgaagtgatagtattaattccactgcctttggtagaggaaagtgttaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                                <  2:313360‑M2/50‑1 (MQ=255)                                               catgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGa                                                                                            >  2:48377‑M2/96‑149 (MQ=255)                                                atgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                           >  1:199180‑M2/95‑149 (MQ=255)                                                    tattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGa                                                                                       <  1:425201‑M2/59‑1 (MQ=255)                                                             cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgcaaaATAATAATCATTTGGTAAATTAGTGTGCAGTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGc                                                                              <  2:189522‑M2/68‑1 (MQ=255)                                                                 tcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAg                                                                          <  1:165264‑M2/72‑1 (MQ=255)                                                                             gcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                              <  2:357027‑M2/84‑1 (MQ=255)                                                                                  ctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTATGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                         >  2:512142‑M2/61‑149 (MQ=255)                                                                                     aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTCTGACAAAGATTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                      >  1:120559‑M2/58‑149 (MQ=255)                                                                                       gaataattgaaatgatattattaattcaactgcatttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAACGATAGACATGCCTAGCCAATCTCTATTTgattgaata                                                    >  2:279308‑M2/56‑148 (MQ=255)                                                                                                aaatgatattattaattccactgcctttggcgggcgggagttctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATGGAAAGAtgt                                           >  1:383525‑M2/47‑149 (MQ=255)                                                                                                   tgctattattaattcaactgtctttgcgagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGTATTTCAGTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAGTCTCTATTTTATTGAATTGAAAGAtgtttg                                        <  2:300724‑M2/106‑1 (MQ=255)                                                                                                    gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTGATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAACAAtgtttgt                                       >  2:474850‑M2/43‑149 (MQ=255)                                                                                                            taattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                               <  1:279308‑M2/115‑1 (MQ=255)                                                                                                             aattccagtgccttgtgtagagggaagtggtaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGTAACTGTAATCAGAAAAGATAGACATGATTAGCAAATGTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                              <  2:159759‑M2/116‑1 (MQ=255)                                                                                                              attccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTTCCTTTCACTACTGGAACTGTAATCAGAAAAGATAAACATGCTTAGCCAATCTCTATTTGATTAAATTGAAAGATGTTTTTTAAGGCATgg                             >  1:454411‑M2/33‑149 (MQ=255)                                                                                                               ctccattgcctgtggtagatgaaagtgttaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTTATTGAATTGAAAGATGTTTGTTAAGGCATGGa                            <  2:155518‑M2/118‑1 (MQ=255)                                                                                                                  cactgcctttggttgaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGc                         <  2:129644‑M2/121‑1 (MQ=255)                                                                                                                     tgcctttggtagatgaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAGGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAg                      <  1:100544‑M2/124‑1 (MQ=255)                                                                                                                         tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                  <  1:112517‑M2/128‑1 (MQ=255)                                                                                                                              tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATTCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGTCATGGATGCAAGCTATATAtt             >  2:206694‑M2/17‑149 (MQ=255)                                                                                                                               agaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCCCTATTTGAATTACTTGAACGATGTTCGTTAAGGCATGGATGCAAGCTATAGattt            >  1:327408‑M2/16‑148 (MQ=255)                                                                                                                                  ggaaagtgtgaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGa         <  2:174280‑M2/137‑1 (MQ=255)                                                                                                                                         tctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTc  <  2:363098‑M2/144‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                ATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTC  >  NC_000913_3_pae_tpiA/1300557‑1300841

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: ‑