New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 3652533NA (NA)199 (2.500) 78/100 0.0 NA noncoding (1443/1443 nt) IS150 repeat region
?REL606 = 3697156 NA (NA)coding (280/4134 nt) rhsA rhsA element core protein RshA

ACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGA  >  REL606/3652487‑3652583
                                              |                                                  
aCCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACt                                                >  1:5599023/1‑51 (MQ=35)
aCCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACt                                                >  1:363232/1‑51 (MQ=35)
aCCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACt                                                <  1:3136162/51‑1 (MQ=35)
 ccTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACtt                                               <  1:6948341/51‑1 (MQ=38)
 ccTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACtt                                               >  1:1895241/1‑51 (MQ=38)
 ccTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACtt                                               >  1:4427244/1‑51 (MQ=38)
 ccTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACtt                                               <  1:6679009/51‑1 (MQ=38)
  cTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACttt                                              <  1:2496635/51‑1 (MQ=40)
  cTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACttt                                              >  1:1944380/1‑51 (MQ=40)
   tataTGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTg                                             <  1:2088673/51‑1 (MQ=255)
    atatGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGa                                            <  1:5451025/51‑1 (MQ=255)
    atatGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGa                                            <  1:1917706/51‑1 (MQ=255)
    atatGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGa                                            >  1:2471339/1‑51 (MQ=255)
      atGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGAtt                                          <  1:3452994/51‑1 (MQ=255)
       tGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGAttt                                         <  1:3880196/51‑1 (MQ=255)
        gCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTta                                        <  1:2665326/51‑1 (MQ=255)
        gCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTta                                        <  1:6949524/51‑1 (MQ=255)
          cTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTtata                                      >  1:86623/1‑51 (MQ=255)
          cTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTtata                                      >  1:6681204/1‑51 (MQ=255)
          cTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTtata                                      >  1:1449003/1‑51 (MQ=255)
           tCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAg                                     >  1:1528866/1‑51 (MQ=255)
              tgtTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCa                                  <  1:211509/51‑1 (MQ=255)
                tttAACTGTGCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAgg                                <  1:1229226/51‑1 (MQ=255)
                tttAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAgg                                >  1:539704/1‑51 (MQ=255)
                tttAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAgg                                >  1:4709190/1‑51 (MQ=255)
                 ttAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGt                                    <  1:1354956/46‑1 (MQ=255)
                 ttAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGt                               >  1:6228384/1‑51 (MQ=255)
                  tAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTg                              <  1:3759882/51‑1 (MQ=255)
                  tAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTg                              >  1:5795501/1‑51 (MQ=255)
                   aaCTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTgg                             >  1:6196596/1‑51 (MQ=255)
                   aaCTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTgg                             >  1:6892646/1‑51 (MQ=255)
                    aCTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTggg                            >  1:4239113/1‑51 (MQ=255)
                     cTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTgggg                           <  1:5606119/51‑1 (MQ=255)
                     cTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTgggg                           <  1:1705504/51‑1 (MQ=255)
                      tGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGc                          <  1:4847386/51‑1 (MQ=255)
                       gTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCt                         <  1:2947147/51‑1 (MQ=255)
                       gTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCt                         <  1:781552/51‑1 (MQ=255)
                        tCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCtt                        <  1:1432166/51‑1 (MQ=255)
                         ccAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCttt                       >  1:26653/1‑51 (MQ=255)
                          cAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCtttt                      <  1:5288585/51‑1 (MQ=255)
                          cAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCtttt                      >  1:3798786/1‑51 (MQ=255)
                          cAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCtttt                      <  1:4815954/51‑1 (MQ=255)
                           aaCTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtc                     <  1:4901984/51‑1 (MQ=255)
                           aaCTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtc                     >  1:2200599/1‑51 (MQ=255)
                           aaCTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtc                     >  1:4559184/1‑51 (MQ=255)
                           aaCTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtc                     <  1:1806531/51‑1 (MQ=255)
                            aCTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtct                    >  1:5270898/1‑51 (MQ=255)
                            aCTTTTGGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtct                    <  1:2748658/51‑1 (MQ=255)
                             cTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtctc                   >  1:4899816/1‑51 (MQ=255)
                             cTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTtctc                   <  1:5549763/51‑1 (MQ=255)
                              tttttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTctct                  >  1:4389400/1‑51 (MQ=255)
                               ttttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctg                 <  1:5169398/51‑1 (MQ=255)
                               ttttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctg                 <  1:6679129/51‑1 (MQ=255)
                                tttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgt                >  1:637861/1‑51 (MQ=255)
                                tttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgt                <  1:2829722/51‑1 (MQ=255)
                                tttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgt                <  1:5157805/51‑1 (MQ=255)
                                 ttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgtc               <  1:5025188/51‑1 (MQ=255)
                                 ttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgtc               >  1:4182725/1‑51 (MQ=255)
                                 ttGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgtc               <  1:3378786/51‑1 (MQ=255)
                                  tGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCtctgtct              >  1:216416/1‑51 (MQ=255)
                                    gggTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGc            <  1:2729231/51‑1 (MQ=255)
                                      gTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCt          >  1:681503/1‑51 (MQ=255)
                                        cAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCttt        <  1:6344595/51‑1 (MQ=255)
                                        cAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCttt        >  1:672035/1‑51 (MQ=255)
                                        cAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCttt        <  1:1835712/51‑1 (MQ=255)
                                         aGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTc       <  1:2761222/51‑1 (MQ=255)
                                         aGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTc       <  1:7266351/51‑1 (MQ=255)
                                         aGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTc       >  1:5527581/1‑51 (MQ=255)
                                         aGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTc       <  1:5722381/51‑1 (MQ=255)
                                          gTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCg      <  1:5275974/51‑1 (MQ=255)
                                          gTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCg      <  1:4218338/51‑1 (MQ=255)
                                           tACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCgg     >  1:1193064/1‑51 (MQ=255)
                                            aCAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGt    <  1:6396654/51‑1 (MQ=255)
                                            aCAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGt    <  1:2189284/51‑1 (MQ=255)
                                             cAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTg   >  1:7268812/1‑51 (MQ=255)
                                              aaaCTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGa  <  1:132991/51‑1 (MQ=255)
                                              aaaCTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGa  >  1:952541/1‑51 (MQ=255)
                                              |                                                  
ACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGA  >  REL606/3652487‑3652583

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.