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)	49 (0.840)	41/276	0.5	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

GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_tpiA/1300553‑1300843                                                                                                                                                  |                                                                                                                                                  tcaaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                                >  1:3864‑M2/146‑149 (MQ=255)            ttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGt                                                                                                                                     >  1:533359‑M2/135‑149 (MQ=255)               gttataagtatttccttaacttgttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaa                                                                                                                                  <  1:740874‑M2/18‑1 (MQ=255)                  ataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaatgattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAGatt                                                                                                                               >  1:264369‑M2/129‑149 (MQ=255)                    aaggatttccttaactgctgctcctcaccttcatgttatttttgccacatcataatcctgggctggctgcagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattat                                                                                                                             <  2:264113‑M2/23‑1 (MQ=255)                       gatttccttaactgcttctcctcaccatcatgttattttcatcatatcataatcctaggcttgctgaagaataattgaaattatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgt                                                                                                                          <  2:117805‑M2/26‑1 (MQ=255)                                  ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                               <  1:668794‑M2/37‑1 (MQ=255)                                  ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgataatattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                               >  1:671687‑M2/113‑149 (MQ=255)                                        ctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                         <  2:961231‑M2/43‑1 (MQ=255)                                           ctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagagaaaagtgctaaATAATAATCAATTGTTGACTCATTGTGCATTTCACTACTGGGACTg                                                                                                      >  1:813129‑M2/104‑149 (MQ=255)                                           ctcaccatcatgttattttcgccaaattaggatccggggcttgctgaagaataattgaattgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTGCACTACTGGAActa                                                                                                      >  2:9468‑M2/104‑148 (MQ=255)                                            tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCCCTACTGGAACTGt                                                                                                     >  2:744255‑M2/103‑149 (MQ=255)                                            tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGt                                                                                                     >  1:437601‑M2/103‑149 (MQ=255)                                              accatcatgttattttcgccacatcataatcctgggcttgctgcagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTTGAACTTTaa                                                                                                   >  2:344108‑M2/101‑149 (MQ=255)                                                     tgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTATGCATTTCCCTACTGTAActgtaatactaaa                                                                                            >  2:275543‑M2/94‑143 (MQ=255)                                                      gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaaa                                                                                           <  1:931107‑M2/57‑1 (MQ=255)                                                           tttcgccacatcataatcctgggcttggtgaagaataatttaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAg                                                                                      <  2:496448‑M2/62‑1 (MQ=255)                                                                ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATg                                                                                 >  1:757276‑M2/83‑149 (MQ=255)                                                                       ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGcc                                                                          >  1:1029500‑M2/76‑149 (MQ=255)                                                                          aaccagggcttgctgaagaataattgaaatgatattatttattctactgactttggtagagtaaagtgctaaAAAACAATCAATTGTTAAATTATTGTGCATTTCACTACTCGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAt                                                                       <  2:103904‑M2/77‑1 (MQ=255)                                                                           tcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAtc                                                                      >  1:960650‑M2/72‑149 (MQ=255)                                                                                ggcttgctgaagaataattgaaatgatattattaattccactgccttttgtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAt                                                                 <  2:468997‑M2/83‑1 (MQ=255)                                                                                 gcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGTAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                                >  2:691674‑M2/66‑149 (MQ=255)                                                                                  cttgcggaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                               <  2:941352‑M2/85‑1 (MQ=255)                                                                                  cttgcataaaaataattgaaatgatattatcaattccactgcctttggtagaggaaagtgataaATAATAATCAATAGTTAAATTATTGGGCAGTTCACTACTGGAGCTGTAATCAGAAAAGATAGACATGCTTAGCCAATCGCTAttt                                                               <  2:941475‑M2/85‑1 (MQ=255)                                                                                    tgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                             <  1:756688‑M2/87‑1 (MQ=255)                                                                                    tgaggaagaataattgaaatgatattagtaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                             <  2:342702‑M2/87‑1 (MQ=255)                                                                                      ctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                           <  2:437601‑M2/89‑1 (MQ=255)                                                                                         aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaa                                                        >  1:405362‑M2/58‑149 (MQ=255)                                                                                           gaataattgaaatgatcttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaatt                                                      >  2:914502‑M2/56‑149 (MQ=255)                                                                                             ataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaattga                                                    >  1:749552‑M2/54‑149 (MQ=255)                                                                                              taattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTCCTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTgattgaattgac                                                   >  1:845648‑M2/53‑148 (MQ=255)                                                                                              taattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGAttgaattgaa                                                   >  2:259968‑M2/53‑149 (MQ=255)                                                                                                attgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTCTAATCAGAAAAGATAGACATCCTTAGCCAATCTCTatttgattgcattcaccg                                                 >  2:105982‑M2/51‑144 (MQ=255)                                                                                                 ttgaaatgatattattaattccactgccttttgtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGa                                                <  1:655846‑M2/100‑1 (MQ=255)                                                                                                 ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGa                                                >  2:203501‑M2/50‑149 (MQ=255)                                                                                                  tgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                               >  2:945523‑M2/49‑149 (MQ=255)                                                                                                  tgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                               >  2:949944‑M2/49‑149 (MQ=255)                                                                                                      atgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                           <  1:88043‑M2/105‑1 (MQ=255)                                                                                                            ttatttattacactgcctttggtcgaggaacgccataaAACATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGACCTGTCCTCGGAAAGGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAg                                     <  1:91621‑M2/111‑1 (MQ=255)                                                                                                              attaattccactgcctttggtagaggaaagtgctaaATAATAATCCCTTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTCTTTGCTTCAATtaaaaactgtttgcaaacac                                   >  2:937195‑M2/37‑142 (MQ=255)                                                                                                              attaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGACAATCTCTATTTGCTTGAATTGACAGATGTTTGTTAAGGc                                   >  1:588393‑M2/37‑149 (MQ=255)                                                                                                                taattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                                 <  2:647070‑M2/115‑1 (MQ=255)                                                                                                                    tccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt                             <  1:296376‑M2/119‑1 (MQ=255)                                                                                                                       actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGGTTGAATTGAAAGATGTTTGTTAAGGCATGGATGCa                          >  1:878961‑M2/28‑149 (MQ=255)                                                                                                                        cttccttcggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTAAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                         >  2:130332‑M2/27‑149 (MQ=255)                                                                                                                        ctggctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                         <  2:950970‑M2/123‑1 (MQ=255)                                                                                                                             tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    >  1:189936‑M2/22‑149 (MQ=255)                                                                                                                                 gtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAt                >  2:24251‑M2/18‑149 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCaa  >  1:207777‑M2/4‑149 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCaa  >  1:848367‑M2/4‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_tpiA/1300553‑1300843

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.