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)	56 (1.030)	48/274	0.2	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

CAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  >  NC_000913_3_pae_pgi/1299355‑1299645                                                                                                                                                |                                                                                                                                                    cAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                               <  1:36752‑M1/150‑7 (MQ=255)  aaaTTACAGTTAGTTATGAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                               <  2:885003‑M1/149‑7 (MQ=255)  aaaTTACAGTTAGTTATGAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                               >  1:885003‑M1/1‑143 (MQ=255)                  taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattat                                                                                                                              >  2:33388‑M1/1‑127 (MQ=255)                  taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattat                                                                                                                              >  1:788686‑M1/1‑127 (MQ=255)                           ccTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcattt                                                                                                                     >  2:674376‑M1/1‑118 (MQ=255)                            cTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGTAAAGTGCTAAataataatcaattgttaaattattgtgcatttc                                                                                                                    >  1:571835‑M1/1‑117 (MQ=255)                             ttAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCATTGGGTAGAGGAAGGTGCTAAataataacaaattgttaaattattgtgcgtttca                                                                                                                   >  1:681021‑M1/1‑116 (MQ=255)                                 cTGCTTATCCTCACCATCATGTTAGTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactac                                                                                                               >  2:218343‑M1/1‑112 (MQ=255)                                        tcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACCGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaact                                                                                                        >  2:250209‑M1/1‑105 (MQ=255)                                          ctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggcactgt                                                                                                      <  2:219287‑M1/150‑48 (MQ=255)                                           tcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCCTTGGTAGCGGAAAGTGCTCAataataatcaattgttaaattattgtgcatttcactactggacatgta                                                                                                     >  2:520934‑M1/1‑102 (MQ=255)                                             aCCATCATGTTATTTTCGCCACATCATAATCCTGAGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTATAGGAAAAGGCTAAgtaataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                   >  2:499156‑M1/1‑100 (MQ=255)                                               ctgagtgttatTTTCGCCACATCATAATCCTGGTTTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGTAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatca                                                                                                 <  2:738238‑M1/145‑53 (MQ=255)                                               catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactcctggaaatgtactca                                                                                                 >  2:349262‑M1/1‑98 (MQ=255)                                                 tcatGTTATTTTCGCCACATCATAATGCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcaga                                                                                               >  1:145209‑M1/1‑96 (MQ=255)                                                   atGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaa                                                                                             <  2:17817‑M1/150‑57 (MQ=255)                                                    tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGCAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTTGTAGAGGAAAGTGCTAAataataatcaattgttaaataaatattcatttcactactggaactgtaatcagaaaa                                                                                            >  1:44933‑M1/1‑93 (MQ=255)                                                    tGTTATTTTCGCCAAATCATAATCCTGGTTTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                            <  2:243339‑M1/150‑58 (MQ=255)                                                        aTTTTCGCCACAGCACAATCCTGGGCTTGCTGAAGAATAATTGAAATGAAATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagata                                                                                        <  1:674544‑M1/150‑62 (MQ=255)                                                              gCCACAGCATAATCCCGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatg                                                                                  <  1:266083‑M1/150‑68 (MQ=255)                                                                  catcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactaatggaaatgtactcagaaaaaaaagaattgctta                                                                              >  2:400661‑M1/1‑79 (MQ=255)                                                                      atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcaaaaaaaatagacatgcttagaca                                                                          >  2:70629‑M1/1‑75 (MQ=255)                                                                             tGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctcta                                                                   <  1:349262‑M1/150‑83 (MQ=255)                                                                                gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactgtaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                                <  1:429403‑M1/150‑86 (MQ=255)                                                                                      tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataa                                                                                                                                                 <  1:137582‑M1/63‑5 (MQ=255)                                                                                      tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataa                                                                                                                                                 >  2:137582‑M1/1‑59 (MQ=255)                                                                                       gaagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcgcttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaa                                                         >  1:964531‑M1/1‑58 (MQ=255)                                                                                       gaagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaa                                                         >  1:801120‑M1/1‑58 (MQ=255)                                                                                         agaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaatt                                                       <  1:156176‑M1/150‑95 (MQ=255)                                                                                             taatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaa                                                   >  2:682081‑M1/1‑52 (MQ=255)                                                                                             taatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                             >  1:848411‑M1/1‑52 (MQ=255)                                                                                             taatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                             <  2:848411‑M1/92‑41 (MQ=255)                                                                                                ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                                <  1:682081‑M1/150‑102 (MQ=255)                                                                                                ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactataatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                                >  1:477075‑M1/1‑49 (MQ=255)                                                                                                  gAAATGATATTATTAATTCCACTTCCTTGGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaagcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgt                                              <  1:652601‑M1/150‑104 (MQ=255)                                                                                                  gAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgt                                              <  2:145209‑M1/150‑104 (MQ=255)                                                                                                    aaTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                            >  2:946604‑M1/1‑45 (MQ=255)                                                                                                     aTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactcctggaactgtaatcagaaaagatagacatgcttatccaatctctatttgatttaattgaaagatgtttg                                           >  2:838880‑M1/1‑44 (MQ=255)                                                                                                       gATAATATTAGTTGCACTGCGTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgtt                                         <  1:604313‑M1/150‑109 (MQ=255)                                                                                                               taATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatg                                 <  2:571835‑M1/150‑117 (MQ=255)                                                                                                                      aatgcCGTTGGAAGACGAAAGTTCGAAatgataatcaattgttaaattattgttcatgtcagtactggaactgtaatcataaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                          <  2:681021‑M1/148‑124 (MQ=255)                                                                                                                      aCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgtttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                          <  2:795477‑M1/150‑124 (MQ=255)                                                                                                                      aCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                          <  1:218343‑M1/150‑124 (MQ=255)                                                                                                                        ctcttttggtaGAAGAAAGTGCTAAaaaataatcaattgttaaattaatgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagc                        <  1:861146‑M1/146‑126 (MQ=255)                                                                                                                          ccTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagcta                      <  2:654525‑M1/150‑128 (MQ=255)                                                                                                                          ccTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                             <  1:72787‑M1/63‑41 (MQ=255)                                                                                                                          ccTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                             >  2:72787‑M1/1‑23 (MQ=255)                                                                                                                                gTAGAGGAAAGTGCTAAataataatcaattgttctttgattgggcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttacggcatggatgcaagctatagatt                >  1:971993‑M1/1‑17 (MQ=255)                                                                                                                                 tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattc               <  1:674376‑M1/150‑135 (MQ=255)                                                                                                                                 tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattc               >  1:509152‑M1/1‑16 (MQ=255)                                                                                                                                  agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct              <  1:199315‑M1/150‑136 (MQ=255)                                                                                                                                     ggAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgat           >  2:413935‑M1/1‑12 (MQ=255)                                                                                                                                      gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcccatctctatttgattgaattgagagatgtttgttaaggcatggatcacagctatcgattccgcta          >  2:85971‑M1/1‑11 (MQ=255)                                                                                                                                         aGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacgg       <  1:33388‑M1/150‑143 (MQ=255)                                                                                                                                           tGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtc     >  1:90256‑M1/1‑6 (MQ=255)                                                                                                                                              tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtccat  >  2:615549‑M1/1‑3 (MQ=255)                                                                                                                                                |                                                                                                                                                    CAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  >  NC_000913_3_pae_pgi/1299355‑1299645

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.