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)	34 (0.960)	33/278	0.2	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

CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAATA  >  NC_000913_3_pae_tpiA/1300564‑1300845                                                                                                                                       |                                                                                                                                                    ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGt                                                                                                                                       >  1:613201‑M2/135‑149 (MQ=255)  tagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGtt                                                                                                                                      <  2:613201‑M2/16‑1 (MQ=255)     ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaaa                                                                                                                                   <  1:15718‑M2/19‑1 (MQ=255)          aggatttccttaactgcttctcctcaccatcatgttattttcgctacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                              <  1:488508‑M2/24‑1 (MQ=255)           ggatttccttaactgcttctcctccccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccgctgcctttggtagaggaaagtgctaaATAATAATAAATTGTTAAATTATtg                                                                                                                             >  1:570806‑M2/125‑149 (MQ=255)             attttgttaactgctgctcctgaccatcatgtcattttcgcgacatcataatcctgggcttgctgaagaataatggaaagtatattattaattctactgcttttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgtg                                                                                                                           <  2:250273‑M2/27‑1 (MQ=255)                tccttaactgcttctcctctccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAt                                                                                                                        <  1:305416‑M2/30‑1 (MQ=255)                  cttaactgcttctcctcgccatcatgttattttcgacacatcataatccaaggaatgctggcggaaaaataaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAttt                                                                                                                      <  1:25066‑M2/32‑1 (MQ=255)                   ttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattaaaatgatattattaattccactgcctttggtagaggaaggtgctaaATAATAATCAATTGTTAAATTATTTTGAATTTc                                                                                                                     >  2:493902‑M2/117‑149 (MQ=255)                      actgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccattacctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCact                                                                                                                  <  1:349375‑M2/36‑1 (MQ=255)                      actgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCact                                                                                                                  >  1:401073‑M2/114‑149 (MQ=255)                               cctcgccatcatgttaatttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACt                                                                                                         <  2:531616‑M2/45‑1 (MQ=255)                                       tcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAg                                                                                                 >  1:432784‑M2/97‑149 (MQ=255)                                         atgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                               <  1:622381‑M2/55‑1 (MQ=255)                                               ttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                         <  1:616730‑M2/61‑1 (MQ=255)                                                         atcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTa                                                                               >  2:429911‑M2/79‑149 (MQ=255)                                                               atcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAt                                                                         <  1:168812‑M2/77‑1 (MQ=255)                                                               atcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAATTAGACATGCTTAGCCAAt                                                                         >  2:254471‑M2/73‑149 (MQ=255)                                                                              aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                          >  1:475364‑M2/58‑149 (MQ=255)                                                                                    aattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGaaa                                                    <  2:113304‑M2/98‑1 (MQ=255)                                                                                           atgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCATAAAAGATAGGCATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                             <  2:281665‑M2/105‑1 (MQ=255)                                                                                             gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgt                                           >  1:218792‑M2/43‑149 (MQ=255)                                                                                                 ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAg                                       <  2:50137‑M2/111‑1 (MQ=255)                                                                                                   attaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGc                                     >  2:586880‑M2/37‑149 (MQ=255)                                                                                                     taattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                                   >  1:321532‑M2/35‑149 (MQ=255)                                                                                                           cactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGTCATGCTTAGCCAATCTCTATTTGATTGACTCGAAAGATGTTTGTTAAGGCCTGGATGc                             >  1:5814‑M2/29‑149 (MQ=255)                                                                                                            actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATAATCATTCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCa                            >  1:289037‑M2/28‑149 (MQ=255)                                                                                                              tgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTCTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAg                          <  1:594267‑M2/124‑1 (MQ=255)                                                                                                                  attggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                      >  1:192731‑M2/22‑149 (MQ=255)                                                                                                                   ttggtagaggaaagtgataaATAATAATCAATTGTTAAAGTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata                     <  2:533677‑M2/129‑1 (MQ=255)                                                                                                                      gtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAt                  >  2:253029‑M2/18‑149 (MQ=255)                                                                                                                            gaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGAt            <  2:401073‑M2/138‑1 (MQ=255)                                                                                                                              aagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATAc          <  1:133938‑M2/140‑1 (MQ=255)                                                                                                                               agtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg         >  2:294524‑M2/9‑149 (MQ=255)                                                                                                                                    taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCCATTTGATGGAATTGAAAGATGTTTGTTAAGGCATGGATGGAAGATGTAGATTCTGATACGctcga    >  1:521058‑M2/4‑147 (MQ=255)                                                                                                                                      aATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAACCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTTTAGATTCTGATACGGTCAATa  >  2:406049‑M2/2‑149 (MQ=255)                                                                                                                                       |                                                                                                                                                    CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAATA  >  NC_000913_3_pae_tpiA/1300564‑1300845

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: ‑
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.