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)	55 (1.070)	48/276	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

GGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAATA  >  NC_000913_3_pae_tpiA/1300555‑1300845                                                                                                                                                |                                                                                                                                                    aaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataata                                                                                                                                                <  1:327993‑M2/6‑1 (MQ=255)  aattacagttagttataaggatttccctaactgctgctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataa                                                                                                                                               <  1:196497‑M2/7‑1 (MQ=255)        agtatgttatagcgattctcttaactgcttcttctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataatttaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                         <  1:90586‑M2/13‑1 (MQ=255)             gttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaa                                                                                                                                    >  2:21602‑M2/132‑149 (MQ=255)                ataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtaaaggaaagtgctaaATAATAATCAATTGTTACatt                                                                                                                                 >  2:62916‑M2/129‑149 (MQ=255)                  aaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgcgaaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattat                                                                                                                               >  1:132036‑M2/127‑149 (MQ=255)                     gatttccttaactcctactcctaaccatcatgttattttcgccacatcataatcctgggcctgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgt                                                                                                                            <  1:896747‑M2/26‑1 (MQ=255)                        ttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                                         <  1:92982‑M2/29‑1 (MQ=255)                        ttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                                         >  2:132107‑M2/121‑149 (MQ=255)                           cttaactgcttctcctcaccatcatgttattttcgccacatcataatcctggggttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAttt                                                                                                                      >  1:614512‑M2/118‑149 (MQ=255)                                   cttcgcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTg                                                                                                              <  1:244590‑M2/40‑1 (MQ=255)                                    ttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTgg                                                                                                             >  1:81451‑M2/109‑149 (MQ=255)                                      ctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                           <  2:614219‑M2/43‑1 (MQ=255)                                            cccgtcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgaccttgctacaggaaagtgccaaATAATAACCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTaa                                                                                                     <  1:39595‑M2/49‑1 (MQ=255)                                            accatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTaa                                                                                                     <  2:614512‑M2/49‑1 (MQ=255)                                             ccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                                    <  1:494727‑M2/50‑1 (MQ=255)                                             ccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                                    <  1:806764‑M2/50‑1 (MQ=255)                                              catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTTTTGTGCATTTCACTACTGGAACTGTAatg                                                                                                   >  2:796081‑M2/99‑148 (MQ=255)                                              catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATc                                                                                                   <  2:446674‑M2/51‑1 (MQ=255)                                                     ttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAg                                                                                            >  2:509616‑M2/92‑149 (MQ=255)                                                           tcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGAc                                                                                      <  1:132107‑M2/64‑1 (MQ=255)                                                                    cataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                             >  2:830254‑M2/77‑149 (MQ=255)                                                                     ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGcc                                                                            >  1:679602‑M2/76‑149 (MQ=255)                                                                      taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaCTCATAATCACTTGTTAGATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAAACATGCTTAGCCa                                                                           >  2:574277‑M2/75‑149 (MQ=255)                                                                        atcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAt                                                                         <  1:172338‑M2/77‑1 (MQ=255)                                                                               tgttgctgaaggatgattgaaatgatagtcataattcctctgcctttggtagaggaaagtgctaaATAATAATCAAATGTTAAATTATTGTGCATTTCACGACTGGAACTTTAAGCAGAAAAGATAGGCATGCTTAGCCAATCTCTAtt                                                                  <  2:409522‑M2/84‑1 (MQ=255)                                                                                cttgcttaataataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                                 <  1:307023‑M2/85‑1 (MQ=255)                                                                                cttgctgaagaagaattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCCAttt                                                                 <  1:337275‑M2/85‑1 (MQ=255)                                                                                   gctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgat                                                              <  1:478785‑M2/88‑1 (MQ=255)                                                                                    ctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                             <  1:549313‑M2/89‑1 (MQ=255)                                                                                      gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAACGATAGACATGCTTAGCCAATCTCTATttgattga                                                           >  1:866545‑M2/59‑149 (MQ=255)                                                                                       aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                          <  1:509616‑M2/92‑1 (MQ=255)                                                                                          aataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGAAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTCTTTGattgaattg                                                       >  2:122870‑M2/55‑149 (MQ=255)                                                                                               ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                          >  1:494637‑M2/50‑141 (MQ=255)                                                                                               ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                          <  2:494637‑M2/92‑1 (MQ=255)                                                                                                tgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                                 <  1:765144‑M2/101‑1 (MQ=255)                                                                                                    atgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                             <  2:81451‑M2/105‑1 (MQ=255)                                                                                                      gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAt                                                                                                                                          >  2:713428‑M2/43‑54 (MQ=255)                                                                                                      gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAt                                                                                                                                          <  1:713428‑M2/12‑1 (MQ=255)                                                                                                      gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgt                                           <  1:587338‑M2/107‑1 (MQ=255)                                                                                                          ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgt                                                                                                                            <  2:376725‑M2/26‑1 (MQ=255)                                                                                                          ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgt                                                                                                                            >  1:376725‑M2/39‑64 (MQ=255)                                                                                                           tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGAATGAATTGAAAGATGTTTGTTAAgg                                      >  1:906193‑M2/38‑149 (MQ=255)                                                                                                                     actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCa                            >  2:314050‑M2/28‑149 (MQ=255)                                                                                                                      ctttctttggtagaggaaagtgctaaATAATAATCAATTGGTAAAATATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGACAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                           <  2:75007‑M2/123‑1 (MQ=255)                                                                                                                      ctgccgttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                           <  2:633721‑M2/123‑1 (MQ=255)                                                                                                                          ctttggtagaggaaagtgctaaCTAATAATCAATTTTTAAATGATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCta                       >  2:925318‑M2/23‑149 (MQ=255)                                                                                                                                tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGa                                >  2:375868‑M2/17‑134 (MQ=255)                                                                                                                                tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGa                                <  1:375868‑M2/118‑1 (MQ=255)                                                                                                                                  gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGTCATGGATGCAAGCTATAGATTCt               <  1:927535‑M2/135‑1 (MQ=255)                                                                                                                                  gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCt               >  2:404138‑M2/15‑149 (MQ=255)                                                                                                                                     gaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTATCCAACGTGTGTTAAGGCATGGATGCAAGCTATAGATTCTGAt            <  1:925318‑M2/138‑1 (MQ=255)                                                                                                                                      aaagtgctaaATAATAATCGATTGATAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATa           <  1:623212‑M2/139‑1 (MQ=255)                                                                                                                                          tgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt       >  1:722413‑M2/7‑149 (MQ=255)                                                                                                                                          tgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt       >  1:722434‑M2/7‑149 (MQ=255)                                                                                                                                               aATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAAATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATCAGGTCAATa  >  1:855782‑M2/2‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                    GGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAATA  >  NC_000913_3_pae_tpiA/1300555‑1300845

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: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.