New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 21877970 (0.680)12 (0.160) 4/36 NT 15.1% coding (669/711 nt) cutF lipoprotein involved with copper homeostasis and adhesion
?REL606 4525951 = 82 (1.060)intergenic (+8/‑59) fimC/fimD chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis

CGGTGCGCCGACTAAAGTATTGGCACCCGATACGGCAGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  REL606/218740‑218779
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcagggGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  >  REL606/4525951‑4525984
                                                                          
CGGTGCGCCGACTAAAGTATTGGCACCCGATACGG                                         >  1:2245122/1‑35
CGGTGCGCCGACTAAAGTATTGGCACCCGATACGG                                         <  1:2925619/35‑1
CGGTGCGCCGACTAAAGTATTGGCACCCGATACGG                                         <  1:11581736/35‑1
CGGGGCGCCGACTAAAGTATTGGCACCCGATACGG                                         <  1:3042471/35‑1
 gggGCGCCGACTAAAGTATTGGCACCCGATACGGC                                        <  1:13218651/32‑1
 GGTGCTCCGACTAAAGTATTGGCACCCGATACGGC                                        >  1:19879778/1‑35
 GGTGCGCCGACTAAAGTATTGGCACCCGATACGGC                                        >  1:18606301/1‑35
  GTGCGCCGACTAAAGTATTGGCACCCGATACGGCA                                       >  1:8058567/1‑35
  GTGCGCCGACTAAAGTATTGGCACCCGATACGGCA                                       >  1:12806714/1‑35
   TGCGCCGACTAAAGTATTGGCACCCGATACTGCAG                                      >  1:12101505/1‑35
   TGCGCCGACTAAAGTATTGGCACCCGATACGGCAG                                      >  1:17256132/1‑35
   TGCGCCGACTAAAGTATTGGCACCCGATACGGCAG                                      >  1:970324/1‑35
    GCGCCGACTAAAGTATTGGCACCCGATACGGCAGG                                     <  1:2479793/35‑1
    GCGCCGACTAAAGTATTGGCACCCGATACGGCAGG                                     >  1:4551813/1‑35
    GCGCCGACTAAAGTATTGGCACCCGATACGGCAGG                                     >  1:825129/1‑35
    GCGCCGACTAAAGTATGGGCACCCGATACGGCAGG                                     <  1:10461367/35‑1
     CGCCGACTAAAGTATTGGCGCCCGATACGGCAGGG                                    <  1:9156747/35‑1
     CGCCGACTAAAGTATTGGCACCCGATACGGCAGGG                                    >  1:13880529/1‑35
     CGCCGACTAAAGTATTGGCACCCGATACGGCAGGG                                    <  1:8391993/35‑1
     CGCCGACTAAAGTATTGGCACCCGATACGGCAGGG                                    <  1:9074727/35‑1
     CGCCGACTAAAGTATTGGCACCCGATACGGCAGGG                                    <  1:11623455/35‑1
     CGCCGACTAAAGTATTGGCACCCGATACGGCAGGG                                    <  1:10947385/35‑1
      GCCGACTAAAGTATTGGCACCCGATACGGCAGGGG                                   >  1:19174817/1‑35
      GCCGACTAAAGTATTGGCACCCGATACGGCAGGGG                                   >  1:7561081/1‑35
      GCCGACTAAAGTATTGGCACCCGATACGGCAGGGG                                   >  1:1473598/1‑35
      GCCGACTAAAGTATTGGCACCCGATACGGCAGGGG                                   >  1:16399097/1‑35
       CCGACTAAAGTATTGGCACCCGATACGGCAGGGGG                                  >  1:7333334/1‑35
        CGACTAAAGTATTGGCACCCGATACGGCAGGGGaa                                 >  1:18386941/1‑33
        CGACTAAAGTATTGGCACCCGATACGGCAGGGGaa                                 >  1:15791387/1‑33
        CGACTAAAGTATTGGCACCCGATACGGCAGGGGGA                                 >  1:2848623/1‑35
        CGACTAAAGTATTGGCACCCGATACGGCAGGGGGA                                 >  1:14826490/1‑35
         GACTAAAGTATTGGCACCCGATACGGCAGGGGGga                                >  1:12862598/1‑33
         GACTAAAGTATTGGCACCCGATACGGCAGGGGGAt                                >  1:17887183/1‑34
         GACTAAAGTATTGGCACCCGATACGGCAGGGGGAA                                >  1:5695669/1‑35
         GACTAAAGTATTGGCACCCGATACGGCAGGGGAAA                                >  1:2210097/1‑35
         GACTAAAGTATTGGCACCCGATACGGCAGGGGAAA                                >  1:12674645/1‑35
            TAAAGTATTGGCACCCGATACGGCAGGGGGAATTT                             >  1:6944847/1‑35
            TAAAGTATTGGCACCCGATACGGCAGGGGAAATTT                             >  1:10413840/1‑35
             AAAGTATTGGCACCCGATACGGCAGGGGGAGTTTT                            >  1:9596957/1‑35
             AAAGTATTGGCACCCGATACGGCAGGGGGAATTTT                            >  1:2193919/1‑35
             AAAGTATTGGCACCCGATACGGCAGGGGGAATTTT                            >  1:11476071/1‑35
             AAAGTATTGGCACCCGATACGGCAGGGGGAATTTT                            >  1:2175167/1‑35
              AAGTATTGGCACCCGATACGGCAGGGGGAATTTTT                           >  1:16995739/1‑35
              AAGTATTGGCACCCGATACGGCAGGGGGAATTTTT                           >  1:6265302/1‑35
               AGTATTGGCACCCGATACGGCAGGGGGAATTTTac                          >  1:12182402/1‑33
               AGTATTGGCACCCGATACGGCAGGGGGAATTTATC                          >  1:10394355/1‑35
                GTATTGGCACCCGATACGGCAGGGGGAATTTTccc                         >  1:14538603/1‑32
                GTATTGGCACCCGATACGGCAGGGGGAATTTTTCc                         >  1:9533844/1‑34
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTt       >  1:14827107/1‑34
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       >  1:12035112/1‑35
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       >  1:12046180/1‑35
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       >  1:5956050/1‑35
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       <  1:12106845/35‑1
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       <  1:8833600/35‑1
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       <  1:13982802/35‑1
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       >  1:2262202/1‑35
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       <  1:7307019/35‑1
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       <  1:7103780/35‑1
                                  GCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTG       >  1:19480815/1‑35
                                  GCAGGGGGAATTTTTCGCATGAATAAAAAGAATTG       <  1:5504980/35‑1
                                   CAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGA      >  1:7414346/1‑35
                                   CAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGA      >  1:12196897/1‑35
                                   CAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGA      >  1:16638936/1‑35
                                   CAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGA      <  1:4039349/35‑1
                                    AGGGGGAATTTTTCGCCTGAATAAAAAGAATTGAC     >  1:6009889/1‑35
                                    AGGGGGAATTTTTCGCCTGAATAAAAAGAATTGAC     >  1:13332797/1‑35
                                    AGGGGGAATTTTTCGCCTGAATAAAAAGAATTGAC     >  1:1861999/1‑35
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:10329934/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:13412032/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:13882197/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    >  1:14493878/1‑35
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:16321985/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:6146249/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    <  1:3353049/35‑1
                                     GGGGGAATTTTTCGCCTGAATAAAAAGAATTGACT    >  1:4895612/1‑35
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   >  1:20326928/1‑35
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   >  1:18021428/1‑35
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   >  1:2150611/1‑35
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   <  1:14103592/35‑1
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   >  1:11056411/1‑35
                                      GGGGAATTTTTCGCCTGAATAAAAAGAATTGACTG   >  1:10335992/1‑35
                                       GGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  >  1:19197068/1‑35
                                       GGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  >  1:4398098/1‑35
                                       GGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  <  1:12008676/35‑1
                                       GGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  <  1:10361565/35‑1
                                       GGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  <  1:5624506/35‑1
                                                                          
CGGTGCGCCGACTAAAGTATTGGCACCCGATACGGCAGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  REL606/218740‑218779
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcagggGGAATTTTTCGCCTGAATAAAAAGAATTGACTGC  >  REL606/4525951‑4525984

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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.