New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1299498	0 (0.000)	54 (0.900)	42/272	0.5	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_pae_pgi	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

GGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_pgi/1300555‑1300843                                                                                                                                                |                                                                                                                                                  aaattacagttagttataaggatttccttaactgcttctcctcatcatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataata                                                                                                                                              <  2:486881‑M2/6‑1 (MQ=255) aaattacagttagttataaggatttccttaactgcttatactcaccataatgttattttcgccacatcataatcctggacttgatgaagaataattgaaatgatattattaattccactgcatttagtaaaggaaagtggtaactaata                                                                                                                                              >  2:381169‑M2/144‑149 (MQ=255)   attacatttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacttcgtaatcctgggcttgctgaataataattgaaattatactattaattccactgcatttggtagaggacactgctaaataataat                                                                                                                                            <  2:975026‑M2/8‑1 (MQ=255)              ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaaa                                                                                                                                 <  1:349301‑M2/19‑1 (MQ=255)              ttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTaaa                                                                                                                                 >  1:856225‑M2/131‑149 (MQ=255)                 taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgcagaataattgaaatgatattattaattccactgcctttggtagaggatagtgctaaATAATAATCACTTGTTTAatta                                                                                                                              >  2:439202‑M2/128‑149 (MQ=255)                 taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATCATCAATTGTTAAttta                                                                                                                              >  2:985455‑M2/128‑149 (MQ=255)                 taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAatta                                                                                                                              >  2:166477‑M2/128‑149 (MQ=255)                    ggatttccttaactgcttctcctcaccatcatgttattttcgacatatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtg                                                                                                                           <  2:389682‑M2/25‑1 (MQ=255)                        ttccttaattgcttctcctccccatcatgttattttcgcaacatcataatcctgggcttgctgaagaataattgaaatgatattattaatttcactgcctttggttgaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                                       <  2:455098‑M2/29‑1 (MQ=255)                           cttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattactacgacttccatcgcagtagtggtgtgctaaATAATAATCAATTGTTAAATTATTGTGCAttt                                                                                                                    <  1:1060891‑M2/32‑1 (MQ=255)                               actgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCact                                                                                                                >  2:105105‑M2/114‑149 (MQ=255)                                       tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAAc                                                                                                        >  1:774980‑M2/106‑149 (MQ=255)                                       tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTAATGGAAc                                                                                                        >  1:682604‑M2/106‑149 (MQ=255)                                            accatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTaa                                                                                                   <  1:394579‑M2/49‑1 (MQ=255)                                              catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATc                                                                                                 >  2:1069779‑M2/99‑149 (MQ=255)                                                    gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCaa                                                                                                                                         >  1:613913‑M2/93‑103 (MQ=255)                                                    gttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCaa                                                                                                                                         <  2:613913‑M2/11‑1 (MQ=255)                                                                 catcataatcctgggcttgctgaagaataattgagatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCtt                                                                              >  2:701952‑M2/80‑149 (MQ=255)                                                                         tcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAtc                                                                      <  1:358409‑M2/78‑1 (MQ=255)                                                                           ctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAtctc                                                                    >  2:895595‑M2/70‑149 (MQ=255)                                                                                    ctgaagaataattgaaacgatagtcttcattccactgcctttggttgaggaaagtgctaaATAATAATCACTCGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTCAGCCAATCTCTATttgatt                                                           <  2:911442‑M2/89‑1 (MQ=255)                                                                                      gaagaataattgaaatgatattattaattccactgcctttggtagatgaaagtgcgaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgattga                                                         >  2:259839‑M2/59‑149 (MQ=255)                                                                                        ggaataagtgaaaggatatacataatttaactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATGATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaat                                                       <  2:174410‑M2/93‑1 (MQ=255)                                                                                         gaataattgaaatgatattattaattccactgcctttggtagaggaaagtggtaaATAATAATCAATTGTTAAATTATTGTGTATTTAACTATTGGAAATGTGATCAGGAAAGATAGAAATGCTTAGCTAATTTCTAGTTGgtttaatt                                                      >  2:1069463‑M2/56‑149 (MQ=255)                                                                                         gaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaTTAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaatt                                                      >  1:1016106‑M2/56‑149 (MQ=255)                                                                                         gaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGAATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGACAATCTCTATTTGattgcatt                                                      >  1:1028142‑M2/56‑149 (MQ=255)                                                                                                  aaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                            <  1:576649‑M2/24‑1 (MQ=255)                                                                                                  aaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                            >  2:576649‑M2/47‑70 (MQ=255)                                                                                                    atgagattattaattccactgcctttgggagaggaaagtggtaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                           <  2:524559‑M2/105‑1 (MQ=255)                                                                                                       atattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgtt                                        <  1:105105‑M2/108‑1 (MQ=255)                                                                                                         attattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTaa                                      <  1:439202‑M2/110‑1 (MQ=255)                                                                                                          ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                                       >  2:931060‑M2/39‑67 (MQ=255)                                                                                                          ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTATTCTGAAAAGATAGAAATGCTTAGCCAATCTCTATTTGATTGAATTGAACGATGTTTGTTAAg                                     >  2:555706‑M2/39‑149 (MQ=255)                                                                                                          ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGCTAAATTATTGTGCa                                                                                                                       <  1:931060‑M2/29‑1 (MQ=255)                                                                                                           tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATCGAAAGATGTTTGTTAAgg                                    >  2:735611‑M2/38‑149 (MQ=255)                                                                                                             ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                       >  2:21161‑M2/36‑96 (MQ=255)                                                                                                             ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                       <  1:21161‑M2/61‑1 (MQ=255)                                                                                                                  tccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt                             <  1:701952‑M2/119‑1 (MQ=255)                                                                                                                  tccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt                             <  1:166477‑M2/119‑1 (MQ=255)                                                                                                                     actgcctttggtagaggaaagtgctgaATAATAATCAATTGTTAAAATATTGTGCATTTCACTACTATAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGATAGATGTTTGTTAAGGCATGGATGCa                          >  1:975800‑M2/28‑149 (MQ=255)                                                                                                                       tgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAg                        >  1:207924‑M2/26‑149 (MQ=255)                                                                                                                       tgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAg                        >  2:289806‑M2/26‑149 (MQ=255)                                                                                                                       tgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAg                        <  2:207924‑M2/124‑1 (MQ=255)                                                                                                                         cctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                           >  2:424018‑M2/24‑96 (MQ=255)                                                                                                                         cctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                           <  1:424018‑M2/73‑1 (MQ=255)                                                                                                                          gtttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCta                     <  2:517264‑M2/127‑1 (MQ=255)                                                                                                                                  gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGCACTCGGGCGAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCt             <  1:1056746‑M2/135‑1 (MQ=255)                                                                                                                                  gaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCt             <  1:895595‑M2/135‑1 (MQ=255)                                                                                                                                   aggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTg            >  2:582537‑M2/14‑149 (MQ=255)                                                                                                                                     gaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGAt          >  1:478447‑M2/12‑149 (MQ=255)                                                                                                                                          tgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt     <  2:856225‑M2/143‑1 (MQ=255)                                                                                                                                          tgctaaATAAGAACAAATTGTTCAATTATTGGGCATTTCACTCCTGGAACGGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt     <  1:175529‑M2/143‑1 (MQ=255)                                                                                                                                          ggctaaAGAATAATCAAGTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAGGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt     <  2:81079‑M2/143‑1 (MQ=255)                                                                                                                                             taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCaa  >  1:804264‑M2/4‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                  GGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_pgi/1300555‑1300843

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.