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 (0.940)	49/270	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

TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC  >  NC_000913_3_pae_pgi/1299351‑1299644                                                                                                                                                    |                                                                                                                                                   ctactaaattacaGTGAGGTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAa                                                                                                                                                   <  2:358329‑M1/144‑2 (MQ=255)         ttACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                           <  2:544224‑M1/149‑10 (MQ=255)            cAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaat                                                                                                                                        <  1:88515‑M1/149‑13 (MQ=255)            cAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaat                                                                                                                                        >  1:684318‑M1/1‑137 (MQ=255)                      taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaatta                                                                                                                              >  1:830927‑M1/1‑127 (MQ=255)                               ccTTAACTGCTTCTCCTCACCATCATGTTATTTTAGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattttttggctgt                                                                                                                     >  1:299239‑M1/1‑118 (MQ=255)                                cTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcattt                                                                                                                    <  1:1010125‑M1/149‑33 (MQ=255)                                   aaCTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcac                                                                                                                 <  2:242529‑M1/149‑36 (MQ=255)                                        cTTCTCCTCACCATCATGTTATTTTCGCCACGTAATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAActaataattaattgttaaattattctgcatttaactactg                                                                                                            >  2:517858‑M1/1‑109 (MQ=255)                                               tcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgt                                                                                                     >  2:500829‑M1/1‑102 (MQ=255)                                                 aCCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaa                                                                                                   <  2:684318‑M1/149‑50 (MQ=255)                                                  ccATGATGTTATCTGCGCCTCATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                  <  1:443385‑M1/149‑51 (MQ=255)                                                  ccATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                  <  1:553384‑M1/149‑51 (MQ=255)                                                   catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                            <  1:1001562‑M1/138‑41 (MQ=255)                                                   catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                            >  2:1001562‑M1/1‑98 (MQ=255)                                                       atGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaa                                                                                             <  2:522436‑M1/149‑56 (MQ=255)                                                        tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataatgatcaattgttaaattattgtgctttgcactattggacctctaaacagaaa                                                                                            >  2:535887‑M1/1‑93 (MQ=255)                                                           tATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaaga                                                                                         <  1:656342‑M1/149‑60 (MQ=255)                                                             ttttCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaataagaaaaatta                                                                                       >  2:254650‑M1/1‑88 (MQ=255)                                                               ttCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTTAAATGATATTAATAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagataga                                                                                     <  2:748587‑M1/149‑64 (MQ=255)                                                                tCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagac                                                                                    <  2:765251‑M1/149‑65 (MQ=255)                                                                   ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactg                                                                                                      <  1:506149‑M1/128‑47 (MQ=255)                                                                   ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactg                                                                                                      >  2:506149‑M1/1‑82 (MQ=255)                                                                    cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                                >  1:759761‑M1/1‑81 (MQ=255)                                                                       accataaTCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                             <  1:156617‑M1/147‑72 (MQ=255)                                                                         catAATCCTGGGCTTGCTGAAGAATAATTTAAATGATATTATTAATTCCACTGCCTCTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcattccactactggcactgtaatcagaaaagatagacatgcttagc                                                                           <  2:814255‑M1/149‑74 (MQ=255)                                                                          atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGACAACGCCAGGGCTCActactcatttattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcc                                                                          >  1:250643‑M1/1‑75 (MQ=255)                                                                                 tGGGCGTGCTGAAGAATAAGTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctct                                                                   <  1:104215‑M1/149‑82 (MQ=255)                                                                                          tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTAGTAGAGGAAAGTGCTAAataataataaattgttaaattattatgcatttcacgaatagagctgtaatcaaaaaagatagacatgcttagccaatctctatttgattg                                                          >  2:119474‑M1/1‑59 (MQ=255)                                                                                            aagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaa                                                        <  2:895471‑M1/149‑93 (MQ=255)                                                                                             agaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagacaaacccgattcgccaatatctatttgattgaat                                                       <  2:784682‑M1/149‑94 (MQ=255)                                                                                                  aatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaa                                                  <  1:500829‑M1/149‑99 (MQ=255)                                                                                                    ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                                >  2:24530‑M1/1‑49 (MQ=255)                                                                                                     tGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                               >  2:378129‑M1/1‑48 (MQ=255)                                                                                                       aaaTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgt                                             >  1:1037669‑M1/1‑46 (MQ=255)                                                                                                         aagatATTATTAATTCCATTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                           <  2:185449‑M1/147‑106 (MQ=255)                                                                                                         aTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                           <  1:858060‑M1/149‑106 (MQ=255)                                                                                                         aTGATATTATTAATGCCGCGTGCTTTGGGAGAGGAACGTGCTAAataataatcaattgttaaattagtgtgcagttcactactggaactgtaatgagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                           <  2:962682‑M1/149‑106 (MQ=255)                                                                                                          tGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttg                                          >  2:976183‑M1/1‑43 (MQ=255)                                                                                                            atatTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcaaatctctatttgattgaattgaaagatgtttgtt                                        <  2:759761‑M1/149‑109 (MQ=255)                                                                                                                tattaATTCCGATGCCTCTGGTAGAGCAAAGTGCTCAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaatatagacatgcttagccaatctctatttgattgaattgaaagaggttggttaagg                                    <  2:423501‑M1/149‑113 (MQ=255)                                                                                                                tattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgaatttcactactggaactgtaatcagaaaagatagaaatgcttagccaatctctatttgattgaattgaaagatgtttgttaagg                                    >  2:477326‑M1/1‑37 (MQ=255)                                                                                                                  ttaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctat                                                                 <  2:220125‑M1/118‑84 (MQ=255)                                                                                                                  ttaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctat                                                                 >  1:220125‑M1/1‑35 (MQ=255)                                                                                                                     aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatgtcttattgattgaattgaaagatgtttgttaaggcatgg                               >  1:559862‑M1/1‑32 (MQ=255)                                                                                                                     aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatgg                               >  2:1009314‑M1/1‑32 (MQ=255)                                                                                                                            tGCCTTTGGTAGAGGAAAGTGCTACctaataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaatgatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaag                        >  2:911520‑M1/1‑25 (MQ=255)                                                                                                                               cTTTGGTATAGGAAAGTGCTAAataataagcaattgttaaattattgtgcatttcactactgtaactgtaatcagaaaagatagacaggcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagcta                     <  1:585719‑M1/149‑128 (MQ=255)                                                                                                                                      agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgcttgttaaggcatggatgcaagctatagattc              <  1:214581‑M1/149‑135 (MQ=255)                                                                                                                                      agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatag                                                                                      >  2:571662‑M1/1‑15 (MQ=255)                                                                                                                                      agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatag                                                                                      <  1:571662‑M1/77‑63 (MQ=255)                                                                                                                                        agGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctg            <  1:378129‑M1/149‑137 (MQ=255)                                                                                                                                        agGAAAGGACTAAacaacaagcaattgttaaagtattgttcattgcactactggaactgtaatcagaaaagatagacattcttagccaatctttatttgattgaattgaaagatgtttgttaagggatggatacaagctagagattctg            <  2:477536‑M1/149‑137 (MQ=255)                                                                                                                                          gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggctgcaagctatagattctgat          >  2:30057‑M1/1‑11 (MQ=255)                                                                                                                                                 cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                  <  1:304837‑M1/54‑51 (MQ=255)                                                                                                                                                 cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                  >  2:304837‑M1/1‑4 (MQ=255)                                                                                                                                                  tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtcaa  >  1:272501‑M1/1‑3 (MQ=255)                                                                                                                                                  tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttattaaggcatggatgcaagctctagattgtgatacggtcaa  >  1:498682‑M1/1‑3 (MQ=255)                                                                                                                                                    |                                                                                                                                                   TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC  >  NC_000913_3_pae_pgi/1299351‑1299644

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.