New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 1590579 =43 (0.420)11 (0.140) 3/38 NT 20.2% intergenic (+294/+147) ydeE/ydeH predicted transporter/hypothetical protein
?REL606 = 3487475 53 (0.650)coding (608/1599 nt) rtcR sigma 54‑dependent transcriptional regulator of rtcBA expression

TACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAA  >  REL606/1590545‑1590612
                                  |                                 
acttcaaccgcatgattgagcagatcgaaaaagtg                                   >  1:6410432‑M1/35‑35 (MQ=255)
acttcaaccgcatgattgagcagatcgaaaaagtg                                   <  1:20521425‑M1/1‑1 (MQ=255)
acttcaaccgcatgattgagcagatcgaaaaagtg                                   <  1:20612514‑M1/1‑1 (MQ=255)
 cttcaaccgcatgattgagcagatcgaaaaagtgg                                  <  1:19016883‑M1/2‑1 (MQ=255)
 aCAGTTGTGTACAAGGGGCCTGATTTTTATTACgg                                  >  1:12502424/1‑35 (MQ=255)
 aCAGTTGTGTACAAGGGGCCTGATTTTTATGACgg                                  >  1:2174466/1‑35 (MQ=255)
 aCAGTTGTGTACAAGGGGCCTGATTTTTATGACgg                                  >  1:11066439/1‑35 (MQ=255)
 aCAGTTGTGTACAAGGGGCCTGATTTTTATGACgg                                  <  1:6419705/35‑1 (MQ=255)
  ttcaaccgcatgattgagcagatcgaaaaagtGGc                                 >  1:10616647‑M1/33‑35 (MQ=255)
  ttcaaccgcatgattgagcagatcgaaaaagtGGc                                 <  1:10278498‑M1/3‑1 (MQ=255)
  ttcaaccgcatgattgagcagatcgaaaaagtGGc                                 >  1:12327083‑M1/33‑35 (MQ=255)
  cAGTTGTGTACAAGGGGCCTGATTTTTATGACGGc                                 <  1:2256361/35‑1 (MQ=255)
  cAGTTGTGTACAAGGGGCCTGATTTTTATGACGGc                                 <  1:17406571/35‑1 (MQ=255)
   tcaaccgcatgattgagcagatcgaaaaagtGGCg                                >  1:4239889‑M1/32‑35 (MQ=255)
   tcaaccgcatgattgagcagatcgaaaaagtGGCg                                >  1:19985045‑M1/32‑35 (MQ=255)
   tcaaccgcatgattgagcagatcgaaaaagtGGCg                                >  1:6572698‑M1/32‑35 (MQ=255)
   aGTTGTGTACAAGGGGCCTGATTTTTATGACGGCg                                <  1:4381530/35‑1 (MQ=255)
    gTTGTGTACAAGGGGCCTGATTTTTATGACGGCGa                               >  1:15113084/1‑35 (MQ=255)
    gTTGTGTACAAGGGGCCTGATTTTTATGACGGCGa                               <  1:10082194/35‑1 (MQ=255)
    gTTGTGTACAAGGGGCCTGATTTTTATGACGGCGa                               <  1:20173026/35‑1 (MQ=255)
    gTTGTGTACAAGGGGCCTGATTTTTATGACGGCGa                               >  1:910892/1‑35 (MQ=255)
    caaccgcatgattgagcagatcgaaaaagtGGCGa                               <  1:10459502‑M1/5‑1 (MQ=255)
    caaccgcatgattgagcagatcgaaaaagtGGCGa                               >  1:13062326‑M1/31‑35 (MQ=255)
    caaccgcatgattgagcagatcgaaaaagtGGCGa                               <  1:9537884‑M1/5‑1 (MQ=255)
     ttGTGTACAAGGGGCCTGATTTTTATGACGGCGaa                              <  1:9580572/35‑1 (MQ=255)
     ttGTGTACAAGGGGCCTGATTTTTATGACGGCGaa                              >  1:14424319/1‑35 (MQ=255)
     ttGTGTACAAGGGGCCTGATTTTTATGACGGCGaa                              <  1:3379516/35‑1 (MQ=255)
     ttGTGTACAAGGGGCATGATTTTTATGACGGCGaa                              <  1:19964684/35‑1 (MQ=255)
     aaccgcattattgagcagatcgaaaaagtGGCGaa                              <  1:13152973‑M1/6‑1 (MQ=255)
     aaccgcatgattgagcagatcgaaaaagtGGCGaa                              <  1:11538492‑M1/6‑1 (MQ=255)
     aaccgcatgattgagcagatcgaaaaagtGGCGaa                              <  1:18750840‑M1/6‑1 (MQ=255)
     aaccgcatgattgagcagatcgaaaaagtGGCGaa                              <  1:17631285‑M1/6‑1 (MQ=255)
      accgcatgattgagcagatcgaaaaagtGGCgaac                             <  1:12537832‑M1/7‑2 (MQ=255)
      accgcatgattgagcagatcgaaaaagtGGCGaaa                             <  1:16137520‑M1/7‑1 (MQ=255)
       gtgtACAAGGGGCCTGATTTTTATGACGGCGaaca                            >  1:11390366/1‑33 (MQ=255)
       gtgtACAAGGGGCCTGATTTTTATGACGGCGaaaa                            >  1:13291639/1‑35 (MQ=255)
        tgtACAAGGGGCCTGATTTTTATGACGGCGaaaaa                           >  1:17658423/1‑35 (MQ=255)
        tgtACAAGGGGCCTGATTTTTATGACGGCGaaaaa                           >  1:13925576/1‑35 (MQ=255)
        tgtACAAGGGGCCTGATTTTTATGACGGCGaaaaa                           <  1:130391/35‑1 (MQ=255)
        tgtACAAGGGGCCTGATTTTTATGACGGCGaaaaa                           >  1:12413054/1‑35 (MQ=255)
        cgcatgattgagcagatcgaaaaagtGgcgaacaa                           <  1:7585344‑M1/9‑4 (MQ=255)
         gtACAAGGGGCCTGATTTTTATGACGGCGaaaaaa                          >  1:16101079/1‑35 (MQ=255)
         gtACAAGGGGCCTGATTTTTATGACGGCGaaaaaa                          >  1:1208261/1‑35 (MQ=255)
         gtACAAGGGGCCTGATTTTTATGACGGCGaaaaaa                          >  1:16961024/1‑35 (MQ=255)
         gcatgattgagcagatcgaaaaagtGGCGaacaaa                          <  1:14658524‑M1/10‑1 (MQ=255)
         gcatgattgagcagatcgaaaaagtGGCGaacaaa                          <  1:10020831‑M1/10‑1 (MQ=255)
         gcatgattgagcagatcgaaaaagtGGCGaaaaaa                          <  1:5027353‑M1/10‑1 (MQ=255)
         gcatgattgagcagatcgaaaaagtGGCGaaaaaa                          <  1:8572953‑M1/10‑1 (MQ=255)
          tACAAGGGGCCTGATTTTTATGACGGGGaaaaaaa                         >  1:18113005/1‑35 (MQ=255)
          catgattgagcagatcgaaaaagtGGCGataaaaa                         <  1:18850492‑M1/11‑1 (MQ=255)
          catgattgagcagatcgaaaaagtGGCGaacaaaa                         <  1:15339911‑M1/11‑1 (MQ=255)
          catgattgagcagatcgaaaaagtGGCGaaaaaaa                         <  1:13633383‑M1/11‑1 (MQ=255)
           aCAAGGGGCCTGATTTTTATGACGGGGaaaaaaaa                        <  1:1161782/35‑1 (MQ=255)
           aCAAGGGGCCTGATTTTTATGACGGCGaaaaaaaa                        >  1:3993371/1‑35 (MQ=255)
           aCAAGGGGCCTGATTTTTATGACGGCGaaaaaaaa                        >  1:13826705/1‑35 (MQ=255)
           aCAAGGGGCCTGATTTTTATGACGGCGaaaaaaaa                        <  1:11649722/35‑1 (MQ=255)
            tgattgagcagatcgaaaaagtGgcgaaaaaatac                       <  1:17610558‑M1/13‑4 (MQ=255)
            tgattgagcagatcgaaaaagtGGCTAAAAAAAAc                       <  1:16179311‑M1/13‑1 (MQ=255)
            tgattgagcagatcgaaaaagtGGCGAACAAAAAc                       <  1:13906628‑M1/13‑1 (MQ=255)
            cAAGGGGCCTGATTTTTATGACGGCGAAAAAAAAc                       <  1:19645974/35‑1 (MQ=255)
            cAAGGGGCCTGATTTTTATGACGGCGAAAAAAAAc                       >  1:10935747/1‑35 (MQ=255)
            cAAGGGGCCTGATTTTTATGACGGCGAAAAAAAAc                       <  1:18599181/35‑1 (MQ=255)
            cAAGGGGCCTGATTTTTATGACGGCGAAAAAAAAc                       <  1:12560400/35‑1 (MQ=255)
            cAAGGGGCCTGATTTTTATGACGGCGAAAAAAAAc                       <  1:12676285/35‑1 (MQ=255)
             gattgagcagatcgaaaaagtGgcgaaaaaaaccc                      <  1:11442122‑M1/14‑4 (MQ=255)
             aaGGGGCCTGATTTTTATGACGGCGAAAAAAAAcc                      <  1:449338/35‑1 (MQ=255)
              attgagcagatcgaaaaagtGGCGAACAAAAaccc                     <  1:2894254‑M1/15‑2 (MQ=255)
              aGGGGCCTGATTTTTATGACGGCGAAAAAAAATCg                     >  1:5399162/1‑35 (MQ=255)
              aGGGGCCTGATTTTTATGACGGCGAAAAAAAACCg                     <  1:5934731/35‑1 (MQ=255)
               ttgagcagatcgaaaaagtGGCGAAAAAACACCGc                    <  1:8406154‑M1/16‑1 (MQ=255)
               ggggCCTGATTTTTATGACGGCGAAAAAAAACCGc                    >  1:19401886/1‑35 (MQ=255)
                tgagcagatcgaaaaagtGGCGAACAAAAACCgcg                   <  1:5325702‑M1/17‑2 (MQ=255)
                tgagcagatcgaaaaagtGGCGAAAAAaaaccccc                   <  1:5680333‑M1/17‑4 (MQ=255)
                tgagcagatcgaaaaagtGGCGAAAAAaaaccacg                   <  1:11552360‑M1/17‑4 (MQ=255)
                gggCCTGATTTTTATGACGGCGAAAAAAAACCGcc                   >  1:7315677/1‑35 (MQ=255)
                gggCCTGATTTTTAAGACGGCGAAAAAAAACCGcc                   >  1:19877848/1‑35 (MQ=255)
                  gCCTGATTTTTATGACGGCGAAAAAAAACCGCCAg                 >  1:14618849/1‑35 (MQ=255)
                  gCCTGATTTTTATGACGGCGAAAAAAAACCGCCAg                 >  1:13468928/1‑35 (MQ=255)
                  gCCTGATTTTTATGACGGCGAAAAAAAACCGCCAg                 >  1:765718/1‑35 (MQ=255)
                   ccTGATTTTTATGACGGCGAAAAAAAACCGCCAGt                >  1:5752957/1‑35 (MQ=255)
                      gATTTTTATGACGGCGAAAAAAAACCGCCAGTaaa             >  1:6503297/1‑35 (MQ=255)
                       aTTTTTATGACGGCGAAAAAAAACCGCCAGTAAAc            >  1:8446364/1‑35 (MQ=255)
                       aTTTTTATGACGGCGAAAAAAAACCGCCAGTAAAc            >  1:8046353/1‑35 (MQ=255)
                        tttttATGACTGCGAAAAAAAACCGCCAGTAAAcc           >  1:2806770/1‑35 (MQ=255)
                        tttttATGACGGCGAAAAAAAACCGCCAGTAAAcc           >  1:15419529/1‑35 (MQ=255)
                        tttttATGACGGCGAAAAAAAACCGCCAGTAAAcc           >  1:1535881/1‑35 (MQ=255)
                         ttttATGACGGCGAAAAAAAACCGCCAGTAAACcg          >  1:1504142/1‑35 (MQ=255)
                          tttATGACGGCGAAAAAAAACCGCCAGTAAACcgg         >  1:6020278/1‑35 (MQ=255)
                           ttATGACGGCGAAAAAAAACCGCCAGTAAACcggc        >  1:18992652/1‑35 (MQ=255)
                            tATGACGGCGAAAAAAAACCGCCAGTAAACcggct       >  1:15354857/1‑34 (MQ=255)
                             aTGACGGCGAAAAAAAACCGCCAGTAAACcggctg      >  1:7358076/1‑33 (MQ=255)
                             aTGACGGCGAAAAAAAACCGCCAGTAAACcggcgg      >  1:18634497/1‑35 (MQ=255)
                             aTGACGGCGAAAAAAAACCGCCAGTAAACcggcgg      >  1:18858119/1‑35 (MQ=255)
                             aTGACGGCGAAAAAAAACCGCCAGTAAACcggcgg      >  1:9774007/1‑35 (MQ=255)
                               gACGGCGAAAAAAAACCGCCAGTAAACcggcgggg    >  1:11607784/1‑33 (MQ=255)
                               gACGGCGAAAAAAAACCGCCAGTAAACcggcgggg    >  1:11027842/1‑33 (MQ=255)
                                aCGGCGAAAAAAAACCGCCAGTAAACcggcggggg   >  1:4835745/1‑32 (MQ=255)
                                 cGGCGAAAAAAAACCGCCAGTAAACCTGCGGTGaa  >  1:7863497/1‑35 (MQ=255)
                                  |                                 
TACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAA  >  REL606/1590545‑1590612

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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.