New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 581288 =99 (0.960)12 (0.150) 3/38 NT 17.1% coding (1672/3144 nt) cusA copper/silver efflux system, membrane component
?REL606 1956195 = 38 (0.470)coding (420/579 nt) flhC DNA‑binding transcriptional dual regulator with FlhD

CAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCAC  >  REL606/1956161‑1956229
                                  |                                  
cAGGCTGGTGAGCGTGGGTAATAAAATTGccgccg                                    >  1:83884/1‑35 (MQ=255)
 aGGCTGGTGAGCGTGGGTAATAAAATTGCcgccgc                                   >  1:13798657/1‑35 (MQ=255)
 aGGCTGGTGAGCGTGGGTAATAAAATTGCcgccgc                                   >  1:12869999/1‑35 (MQ=255)
 aGGCTGGTGAGCGTGGGTAATAAAATTGCcgccgc                                   >  1:12735124/1‑35 (MQ=255)
  ggCTGGTGAGCGTGGGTAATAAAATTGCCGCCgca                                  >  1:1193742/1‑35 (MQ=255)
  ggCTCGTGAGCGTGGGTAATAAAATTGCCGCCgca                                  >  1:8281948/1‑35 (MQ=255)
   gCTGGTGAGCGTGGGTAATAAAATTGCCTCCgcag                                 >  1:18024499/1‑35 (MQ=255)
   gCTGGTGAGCGTGGGTAATAAAATTGCCGCCgcag                                 >  1:11867283/1‑35 (MQ=255)
   gCTGGTGAGCGTGGGTAATAAAATTGCCGCCgcag                                 >  1:18646880/1‑35 (MQ=255)
    cTGGTGAGCGTGGGTAATGAAATTGCCGCCgcagc                                >  1:4850588/1‑35 (MQ=255)
    cTGGTGAGCGTGGGTAATAAAATTGCCGCCgcagc                                >  1:16426215/1‑35 (MQ=255)
     tGGTGAGCGTGGGTAATAAAATTGCCGCCgcagca                               >  1:16229630/1‑35 (MQ=255)
     tGGTGAGCGTGGGTAATAAAATTGCCGCCgcagca                               >  1:2303154/1‑35 (MQ=255)
     tGGTGAGCGTGGGTAATAAAATTGCCGCCgcagca                               >  1:4516273/1‑35 (MQ=255)
      ggTGAGCGTGGGTAATAAAATTGCCGCCGcagcag                              >  1:4793761/1‑35 (MQ=255)
      ggTGAGCGTGGGTAATAAAATTGCCGCCGcagcag                              >  1:5305930/1‑35 (MQ=255)
       gTGAGCGTGGGTAATAAAATTGCCGCCGcagcagg                             >  1:908582/1‑34 (MQ=255)
       gTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGt                             >  1:16314798/1‑35 (MQ=255)
       gTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGt                             >  1:4287862/1‑35 (MQ=255)
       gTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGt                             >  1:16472281/1‑35 (MQ=255)
       gTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGt                             >  1:1279095/1‑35 (MQ=255)
        tGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGtt                            >  1:1220685/1‑35 (MQ=255)
         gAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTg                           >  1:16128113/1‑35 (MQ=255)
         gAGCGTGGGTAATAAAATTGCCGCCGCAGCAGGTg                           >  1:9633259/1‑35 (MQ=255)
          aGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGc                          >  1:7938708/1‑35 (MQ=255)
          aGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGc                          >  1:328820/1‑35 (MQ=255)
          aGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGc                          >  1:9031545/1‑35 (MQ=255)
           gCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGcc                         >  1:161554/1‑34 (MQ=255)
           gCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCa                         >  1:9670343/1‑35 (MQ=255)
            cGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAg                        >  1:18975953/1‑35 (MQ=255)
            cGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAg                        >  1:10144346/1‑35 (MQ=255)
             gttggTAATAAAATTGCCGCCGCAGCAGTTGCAGc                       >  1:13955571/4‑35 (MQ=255)
             gTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAgg                       >  1:3670669/1‑34 (MQ=255)
             gTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGc                       >  1:8478883/1‑35 (MQ=255)
               gggTAATAAAATTGCCGCCGCAGCAGTTGCAGCTg                     >  1:10905789/1‑35 (MQ=255)
               gggTAATAAAATTGCCGCCGCAGCAGGTGGAGCTg                     >  1:13504821/1‑35 (MQ=25)
                 taaaaaaattccccgccGCAGCAGTTGCAGCTGGa                   <  1:1682463‑M2/18‑1 (MQ=255)
                 gTAATAAAATTGCCGCCGCAGCAGTTGCAGCTggg                   >  1:4763544/1‑34 (MQ=255)
                 gTAATAAAATTGCCGCCGCAGCAGTTGCAGCTggg                   >  1:16561800/1‑34 (MQ=255)
                 gTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGa                   >  1:9786080/1‑35 (MQ=255)
                  aaaaaaattccccgccGCAGCAGTTGCAGCTGGaa                  <  1:13300431‑M2/19‑1 (MQ=255)
                   aataaAATTGCCGCCGCAGCAGTTGCAGCTGGaaa                 >  1:5617448/1‑35 (MQ=255)
                   aataaAATTGCCGCCGCAGCAGTTGCAGCTGGaaa                 >  1:11116240/1‑35 (MQ=255)
                   aataaAATTGCCGCCGCAGCAGTTGCAGCTGGaaa                 >  1:19960355/1‑35 (MQ=255)
                   aataaAATTGCCGCCGCAGCAGTTGCAGCTGGaaa                 >  1:17234646/1‑35 (MQ=255)
                   aaaaaattccccgccGCAGCAGTTGCAGCTGGaaa                 <  1:14807839‑M2/20‑1 (MQ=255)
                   aaaaaaatccccgccGCAGCAGTTGCAGCTGGaaa                 <  1:14808121‑M2/20‑1 (MQ=255)
                    aaaaattccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:16950389‑M2/21‑1 (MQ=255)
                    aaaaattccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:4189421‑M2/21‑1 (MQ=255)
                    aaaaagtccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:10757383‑M2/21‑1 (MQ=255)
                    aaaaagtccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:19772725‑M2/21‑1 (MQ=255)
                    aaaaaatccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:20053617‑M2/21‑1 (MQ=255)
                    aaaaaatccccgccGCAGCAGTTGCAGCTGGAAAg                <  1:4444775‑M2/21‑1 (MQ=255)
                     aaaattccccgccGCAGCAGTTGCAGCTGGAAAGt               <  1:6117308‑M2/22‑1 (MQ=255)
                      aaattgcccgccGCAGCAGTTGCAGCTGGAAAGtt              <  1:1471769‑M2/23‑1 (MQ=255)
                      aaaaTTGCCGCCGCAGCAGTTGCAGGTGGGAAggt              >  1:3171469/1‑33 (MQ=25)
                      aaaaTTGCCGCCGCAGCAGTTGCAGCTGGGAAGtt              >  1:13973483/1‑35 (MQ=255)
                      aaaaTTGCCGCCGCAGCAGTTGCAGCTGGAAAggt              >  1:2877186/1‑33 (MQ=255)
                       aaatccccgccGCAGCAGTTGCAGCTGGAAAGTTg             <  1:16125289‑M2/24‑1 (MQ=255)
                       aaaTTGCCGCCGCAGCAGTTGCAGCTGGGAAGTTg             >  1:16606946/1‑35 (MQ=255)
                       aaaTTGCCGCCGCAGCAGTTGCAGCTGGGAAGGTg             >  1:1503578/1‑35 (MQ=37)
                       aaaTTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTg             >  1:7220539/1‑35 (MQ=255)
                        attccccgccGCAGCAGTTGCAGCTGGAAAGTTGc            <  1:5927766‑M2/25‑1 (MQ=255)
                        aaTTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGc            >  1:10393012/1‑35 (MQ=255)
                        aaTTGCCGCCGCAGCAGTTGCAGCTGGAAAGGTGc            >  1:7722999/1‑35 (MQ=255)
                         tcccccgccGCAGCAGTTGCAGCTGGAAAGTTGCa           <  1:2736104‑M2/26‑1 (MQ=255)
                         aTTGCCGCCGCAGCAGTTGCAGCTGGGAAGGTGCa           >  1:2205215/1‑35 (MQ=37)
                          ttGCCGCCGCAGCAGGTGCAGCTGGAAAGTTTCAg          >  1:6893602/1‑35 (MQ=21)
                          tgcccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:19759564‑M2/27‑1 (MQ=255)
                          tccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:13559617‑M2/27‑1 (MQ=255)
                          tccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:10801265‑M2/27‑1 (MQ=255)
                          tccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:7749457‑M2/27‑1 (MQ=255)
                          gccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:1283865‑M2/27‑1 (MQ=255)
                          ccgccgccGCAGCAGTTGCAGCTGGAAAGTTGCAg          <  1:17975263/33‑1 (MQ=255)
                           ccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAGt         <  1:1275676‑M2/28‑1 (MQ=255)
                           ccccgccGCAGCAGTTGCAGCTGGAAAGTTGCAGt         <  1:11704614‑M2/28‑1 (MQ=255)
                            gccgccGCAGCAGTTGCAGCTGGAAAGTTGCAgga        >  1:7948332/1‑33 (MQ=255)
                            cccgccGCAGCAGTTGCAGCTGGAAAGTTGCAGTa        <  1:3458871‑M2/29‑1 (MQ=255)
                             ccgccGCAGCAGTTGCAGCTGGAAAGTTGCAGTaa       <  1:4660255‑M2/30‑1 (MQ=255)
                              cgccGCAGCAGTTGCAGCTGGAAAGTTGCAGgaaa      >  1:6526368‑M2/5‑34 (MQ=255)
                              cgccGCAGCAGTTGCAGCTGGAAAGTTGCAGTAAt      <  1:6041142‑M2/31‑1 (MQ=255)
                               gccGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATc     <  1:11826965‑M2/32‑1 (MQ=255)
                                ccgcAGCAGTTGCAGCTGGGAAGGTGCAGGAATcc    >  1:14332675/1‑35 (MQ=25)
                                ccGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATcc    <  1:6134207‑M2/33‑1 (MQ=255)
                                 cGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCa   <  1:237603‑M2/34‑1 (MQ=255)
                                 cGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCa   <  1:3630984‑M2/34‑1 (MQ=255)
                                  gcagcaGTTTCAGCTGGAAAGTTGCAGGAAACCAc  >  1:3677687/1‑35 (MQ=21)
                                  gcagcaGTTGCAGCTGGAAAGTTGCAGTAATCCAc  <  1:7561780/35‑1 (MQ=255)
                                  gcagcaGTTGCAGCTGGAAAGTTGCAGTAATCCAc  <  1:11898044/35‑1 (MQ=255)
                                  gcagcaGTTGCAGCTGGAAAGTTGCAGTAATCCAc  <  1:5892119/35‑1 (MQ=255)
                                  |                                  
CAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCAC  >  REL606/1956161‑1956229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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.