New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 1204666 =70 (0.680)9 (0.120) 4/36 NT 11.7% coding (481/1461 nt) phoQ sensory histidine kinase in two‑compoent regulatory system with PhoP
?REL606 3975303 = 83 (1.080)coding (677/801 nt) yigL predicted hydrolase

Only 100 of 168 total aligned reads displayed.

GGGATGAACGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGT  >  REL606/3975269‑3975337
                                  |                                  
gggATGAACGATGCCGAAATGCTGTCGATGGCggg                                    >  1:5848374/1‑35 (MQ=255)
gggATGAACGATGCCGAAATGCTGTCGATGGCggg                                    >  1:19313136/1‑35 (MQ=255)
gggATGAACGATGCCGAAATGCTGTCGATGGCggg                                    <  1:10873231/35‑1 (MQ=255)
gggATGAACGATGCCGAAATGCTGTCGATGGCggg                                    >  1:17489070/1‑35 (MQ=255)
gggATGAACGATGCCGAAATGCTGTCGATGGCggg                                    >  1:16878043/1‑35 (MQ=255)
gacgacgacgcggagatgacccactnggtggcggg                                    >  1:16418714‑M2/35‑35 (MQ=255)
gacgacgacgcggagatgacccactcggtggcggg                                    >  1:8281808‑M2/35‑35 (MQ=255)
gacgacgacgcggagatgacccactcggtggcggg                                    >  1:5747865‑M2/35‑35 (MQ=255)
gacgacgacgcggagatgacccactcggtggcggg                                    >  1:14993815‑M2/35‑35 (MQ=255)
  gATGAACGATGCCGAAATGCTGTCGATGGCGGGGa                                  <  1:1738789/35‑1 (MQ=255)
   gacgacgcggagatgacccactcggtggcggGGaa                                 >  1:4223237‑M2/32‑35 (MQ=255)
   gacgacgcggagatgacccactcggtggcggGGaa                                 >  1:7663864‑M2/32‑35 (MQ=255)
   aTGAACGATGCCGAAATGCTGTCGATGGCggggga                                 >  1:20588820/1‑33 (MQ=255)
   aTGAACGATGCCGAAATGCTGTCGATGGCggggga                                 >  1:10530790/1‑33 (MQ=255)
   aTGAACGATGCCGAAATGCTGTCGATGGCGGGGaa                                 <  1:17403789/35‑1 (MQ=255)
   aTGAACGATGCCGAAATGCTGTCGATGGCGGGGaa                                 >  1:7278639/1‑35 (MQ=255)
   aTGAACGATGCCGAAATGCTGTCGATGGCGGGGaa                                 <  1:19822307/35‑1 (MQ=255)
    tGAACGATGCCGAAATGCTGTCGATGGCGGGGaaa                                >  1:16322115/1‑35 (MQ=255)
    tGAACGATGCCGAAATGCTGTCGATGGCGGGGaaa                                <  1:13359798/35‑1 (MQ=255)
    tGAACGATGCCGAAATGCTGTCGATGGCGGGGaaa                                <  1:1516997/35‑1 (MQ=255)
    acgacgcggagatgacccactcggtggcggGGaaa                                >  1:19707923‑M2/31‑35 (MQ=255)
     gAACGATGCCGAAATGCTGTCGATGGCGGGGAAAg                               >  1:6841220/1‑35 (MQ=255)
     cgacgcggagatgacccactcggtggcggggaacg                               >  1:10985356‑M2/30‑33 (MQ=255)
     cgacgcggagatgacccactcggtggcggGGAAAg                               >  1:4835612‑M2/30‑35 (MQ=255)
      aaCGATGCCGAAATGCTGTCGATGGCTGGGAAAgg                              >  1:4062094/1‑35 (MQ=255)
      aaCGATGCCGAAATGCTGTCGATGGCGGGGGAAgg                              >  1:6068426/1‑35 (MQ=255)
      aaCGATGCCGAAATGCTGTCGATGGCGGGGGAAgg                              >  1:16144866/1‑35 (MQ=255)
      aaCGATGCCGAAATGCTGTCGATGGCGGGGAAAgg                              >  1:15233470/1‑35 (MQ=255)
      aaCGATGCCGAAATGCTGTCGATGGCGGGGAAAgg                              >  1:3531356/1‑35 (MQ=255)
       acgcggagatgacccactcggtggcggGGAAAGGc                             >  1:6127730‑M2/28‑35 (MQ=255)
       aCGATGCCGAAATGCTGTCGATGGCGGGGGAAGGc                             >  1:9277401/1‑35 (MQ=255)
       aCGATGCCGAAATGCTGTCGATGGCGGGGGAAGGc                             >  1:11981785/1‑35 (MQ=255)
       aCGATGCCGAAATGCTGTCGATGGCGGGGAAAGGc                             <  1:10386725/35‑1 (MQ=255)
       aCGATGCCGAAATGCTGTCGATGGCGGGGAAAGGc                             <  1:15727061/35‑1 (MQ=255)
       aCGATGCCGAAATGCTGCCGATGGCGGGGAAAGGc                             >  1:18710310/1‑35 (MQ=255)
        cgcggagatgacccactcggtggcggGGaaagtac                            >  1:7814621‑M2/27‑32 (MQ=255)
        cgcggagatgacccactcggtggcggGGAAAGTCt                            >  1:4942248‑M2/27‑35 (MQ=255)
        cgcggagatgacccactcggtggcggGGAAAGGCt                            >  1:18593356‑M2/27‑35 (MQ=255)
        cGATGCCGAAATGCTGTCGATGGCGTGGAAAGGCt                            >  1:1545665/1‑35 (MQ=255)
        cGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCt                            <  1:20137968/35‑1 (MQ=255)
        cGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCt                            <  1:10827026/35‑1 (MQ=255)
        cGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCt                            >  1:3947568/1‑35 (MQ=255)
        cGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCt                            >  1:7448048/1‑35 (MQ=255)
         gATGCCGAAATGCTGTCGATGGCGGGGGAAGGCTg                           >  1:4299843/1‑35 (MQ=255)
         gATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTg                           <  1:18986716/35‑1 (MQ=255)
         gATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTg                           >  1:11569866/1‑35 (MQ=255)
         gATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTg                           <  1:10092518/35‑1 (MQ=255)
         gATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTg                           >  1:10044270/1‑35 (MQ=255)
           tGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCa                         <  1:14324194/35‑1 (MQ=255)
            gCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCAt                        >  1:8346838/1‑35 (MQ=255)
             ccGAAATGCTGTCGATTGCGGGGAAAGGCTGCAtt                       >  1:12217335/1‑35 (MQ=255)
             ccGAAATGCTGTCGATGGCGGGGAAAGGCTGCAtt                       <  1:17188755/35‑1 (MQ=255)
             ccGAAATGCTGTCGATGGCGGGGAAAGGCTGCAtt                       >  1:3540664/1‑35 (MQ=255)
             ccGAAATGCTGTCGATGGCGGGGAAAGGCTGCAtt                       <  1:3129256/35‑1 (MQ=255)
             ccGAAATGCTGTCGATGGCGGGGAAAGGCTGCAtt                       <  1:13599290/35‑1 (MQ=255)
              cGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTa                      >  1:4630612/1‑35 (MQ=255)
              cGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTa                      >  1:19835347/1‑35 (MQ=255)
              cGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTa                      <  1:16800254/35‑1 (MQ=255)
              cGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTa                      >  1:13981108/1‑35 (MQ=255)
               gAAATGCTGTCGATGGCGGGGAAAGGCTGCATTAt                     >  1:19717865/1‑35 (MQ=255)
                aaaTGCTGTCGATGGCGGGGAAAGGCTGCATTATg                    <  1:2012532/35‑1 (MQ=255)
                aaaTGCTGTCGATGGCGGGGAAAGGCTGCATTATg                    <  1:2241384/35‑1 (MQ=255)
                aaaTGCTGTCGATGGCGGGGAAAGGCTGCATTATg                    >  1:8616115/1‑35 (MQ=255)
                  aTGCTGTCGATGGCGGGGAAAGGCTGCATTATggg                  <  1:12600019/35‑1 (MQ=255)
                  aTGCTGTCGATGGCGGGGAAAGGCTGCATTATggg                  <  1:13970303/35‑1 (MQ=255)
                    gCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa                <  1:6734520/35‑1 (MQ=255)
                     cTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg               <  1:9932380/35‑1 (MQ=255)
                     cTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg               <  1:8895695/35‑1 (MQ=255)
                     cTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg               >  1:3038661/1‑35 (MQ=255)
                     cTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg               >  1:18477152/1‑35 (MQ=255)
                      tGTCGATGGCGGGGAAAGGCTGCATTATGGGccgg              >  1:1222906/1‑32 (MQ=255)
                      tGTCGATGGCGGGGAAAGGCTGCATTATGGGccgg              >  1:4079178/1‑32 (MQ=255)
                      tGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt              <  1:15596134/35‑1 (MQ=255)
                      tGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt              <  1:18010986/35‑1 (MQ=255)
                       gTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg             <  1:1110880/35‑1 (MQ=255)
                       gTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg             <  1:19148240/35‑1 (MQ=255)
                       gTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg             <  1:20097350/35‑1 (MQ=255)
                       gTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg             <  1:19439177/35‑1 (MQ=255)
                        tCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc            >  1:17839626/1‑35 (MQ=255)
                        tCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc            <  1:6124758/35‑1 (MQ=255)
                        tCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc            >  1:4026474/1‑35 (MQ=255)
                        tCGATGGCGGGGAAAGGCTGCATTATGGGCAGGgc            >  1:15881822/1‑35 (MQ=255)
                         cGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg           <  1:15208429/35‑1 (MQ=255)
                         cGATGGCGGGGAAAGGCTGCATTATGGGCAGGgcg           >  1:16091805/1‑35 (MQ=255)
                             ggcggGGAAAGGCTGCATTATGGGCAGGGCGCAcc       >  1:6679585‑M2/6‑35 (MQ=255)
                              gcggGGAAAGGCTGCATTATGGGCAGTGCGCACCa      <  1:18292087‑M2/31‑1 (MQ=255)
                              gcggGGAAAGGCTGCATTATGGGCAGTGCGCACCa      <  1:2507790‑M2/31‑1 (MQ=255)
                              gcggGGAAAGGCTGCATTATGGGCAGTGCGCACCa      <  1:5235670‑M2/31‑1 (MQ=255)
                              gcggGGAAAGGCTGCATTATGGGCAGGGCGCACCa      >  1:12720598‑M2/5‑35 (MQ=255)
                               cggGGAAAGGCTGCATTATGGGCAGTGCGCACCAg     >  1:3327994‑M2/4‑35 (MQ=255)
                               cggGGAAAGGCTGCATTATGGGCAGTGCGCACCAg     <  1:4943085‑M2/32‑1 (MQ=255)
                               cggGGAAAGGCTGCATTATGGGCAGGGCGCACCAg     >  1:15502400‑M2/4‑35 (MQ=255)
                                ggGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc    >  1:16020055‑M2/3‑35 (MQ=255)
                                ggGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc    <  1:19891746‑M2/33‑1 (MQ=255)
                                ggGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc    >  1:13849343‑M2/3‑35 (MQ=255)
                                 gGGAAAGGCTGCATTATGGGCAGTGCGCACCCGCg   >  1:11220249‑M2/2‑35 (MQ=255)
                                 gGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCg   <  1:20255355‑M2/34‑1 (MQ=255)
                                 gGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCg   <  1:14548721‑M2/34‑1 (MQ=255)
                                  ggAAAGGCTGCATTATGGGCAGTGCGCACCAGCGt  <  1:11742788/35‑1 (MQ=255)
                                  ggAAAGGCTGCATTATGGGCAGTGCGCACCAGCGt  <  1:9981104/35‑1 (MQ=255)
                                  |                                  
GGGATGAACGATGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGT  >  REL606/3975269‑3975337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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.