New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 125389042 (0.160)37 (0.140) 3/178 40.1 0.36 intergenic (+48/+43) RCAP_rcc01181/hisH hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
?NC_014034 2590190 = 90 (0.310)intergenic (‑89/‑167) glnE/RCAP_rcc02415 glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....C....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253790‑1253955
                                                                                                    |                                                                              
tGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg                                                                                >  2:3963063/1‑101 (MQ=255)
tGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg                                                                                <  2:5073744/101‑1 (MQ=255)
 ggTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....g                                                                          <  2:4455133/101‑1 (MQ=255)
 ggTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGGGCg.....g                                                                          >  2:3721258/1‑101 (MQ=255)
  gTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGACCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gg                                                                         <  2:4129617/101‑1 (MQ=255)
   tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....ggg                                                                        <  1:3721486/101‑2 (MQ=255)
    gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                       <  1:1648087/101‑3 (MQ=255)
    gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                       >  2:3610669/1‑99 (MQ=255)
     cTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTACATACCTCGGGGGTGCG.....GGGg....c                                                                  <  1:3287476/101‑1 (MQ=255)
     cTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c                                                                  <  2:5495142/101‑1 (MQ=255)
      tGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....g                                                             <  2:2879266/101‑1 (MQ=255)
       gggCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gg                                                            <  1:2768421/101‑2 (MQ=255)
        ggCAAGCTCGGCTTCCAGGCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gga                                                           <  1:4407218/101‑3 (MQ=255)
          cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:4237004/1‑97 (MQ=255)
          cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:5655651/1‑97 (MQ=255)
          cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:4540525/1‑97 (MQ=255)
          cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         <  2:2296930/101‑5 (MQ=255)
          cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         <  1:604756/101‑5 (MQ=255)
           aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        <  2:2659941/101‑6 (MQ=255)
           aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        >  2:4611253/1‑96 (MQ=255)
           aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGGGCG.....GGGg....c....ggagcc                                                        >  1:5707759/1‑96 (MQ=255)
           aaGCTCGGCTTCCAGACCGGCTGAGCCTTGGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        <  1:1623746/101‑6 (MQ=38)
            aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccc                                                       >  1:5609830/1‑95 (MQ=255)
            aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccc                                                       <  2:184310/101‑7 (MQ=255)
             gCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccc                                                      >  1:867335/1‑94 (MQ=255)
              cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAACCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccccc                                                     <  2:3528109/101‑9 (MQ=38)
              cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gggcccacc                                                     >  2:1269995/1‑93 (MQ=255)
              cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccccc                                                     <  2:5185018/101‑9 (MQ=255)
              cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccca                                                     <  1:620523/101‑9 (MQ=255)
               tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  1:3619821/1‑92 (MQ=38)
               tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  1:3367476/1‑92 (MQ=38)
               tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  2:650778/1‑92 (MQ=38)
                                           ggCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCg                                 >  2:5356405/1‑101 (MQ=9)
                                           ggCAAAAAAACCCGACCCCGCCCCGCTCTCATCTTCCCCTAAATCCCTGGGGGGTGGGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCg                                 <  2:5065266/101‑1 (MQ=2)
                                               aaaTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAAt                             >  1:2926960/1‑101 (MQ=9)
                                                aaTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATc                            >  2:3570127/1‑101 (MQ=9)
                                                   aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  1:5486119/1‑101 (MQ=9)
                                                   aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  1:5167136/1‑101 (MQ=9)
                                                   aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  2:2042639/1‑101 (MQ=9)
                                                      ccGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCa                      >  1:2946857/1‑101 (MQ=9)
                                                       cGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCAc                     >  1:525419/1‑101 (MQ=9)
                                                       cGACCCCCCCCCTCTCTCATCTTGCCCTAAATCCCCGGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCAc                     <  2:870099/101‑1 (MQ=2)
                                                        gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  2:1658746/1‑101 (MQ=9)
                                                        gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  2:1501532/1‑101 (MQ=9)
                                                        gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  1:1645515/1‑101 (MQ=9)
                                                          tCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGc                  >  1:4579903/1‑101 (MQ=9)
                                                           cccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                 >  2:2974796/1‑101 (MQ=9)
                                                            ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGGAATCCTCTCACGCCtt                >  1:5039673/1‑101 (MQ=9)
                                                            ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  1:1521849/1‑101 (MQ=9)
                                                            ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  2:714134/1‑101 (MQ=9)
                                                            ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  2:5771562/1‑101 (MQ=9)
                                                            ccgccccgcTCTCATCTTGCCCTAAATACCCCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  1:5140933/1‑101 (MQ=2)
                                                             cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc               >  1:1668561/1‑101 (MQ=9)
                                                             cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGATTc               >  2:4096463/1‑101 (MQ=9)
                                                              gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc              >  2:3372749/1‑101 (MQ=9)
                                                              gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc              >  1:3676071/1‑101 (MQ=9)
                                                               ccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCa             >  2:4176033/1‑101 (MQ=9)
                                                                cccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGGTTCCAg            >  2:1086953/1‑101 (MQ=9)
                                                                  cgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGtt          >  2:1218679/1‑101 (MQ=9)
                                                                   tctctCATCTTGCCCTAAATCCCTCGGGGGTGCGGGGGCGGAG....CCCCTGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         <  2:2245326/100‑1 (MQ=9)
                                                                   gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:4297163/1‑101 (MQ=9)
                                                                   gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:2828355/1‑101 (MQ=9)
                                                                   gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:4844535/1‑101 (MQ=9)
                                                                    ctctCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCa        >  1:159353/1‑101 (MQ=9)
                                                                    ctctCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCa        >  2:5198937/1‑101 (MQ=9)
                                                                      ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTTCAGTTCAgg      >  1:2858633/1‑101 (MQ=9)
                                                                       tcATCTTGCCCTAAATACCTCGGGGGCGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGGGAAATCCTCTCACGGCCTCCCGTTcccga     >  1:1301957/1‑97 (MQ=0)
                                                                        cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  2:435806/1‑101 (MQ=9)
                                                                        cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  2:1531976/1‑101 (MQ=9)
                                                                        cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  1:5399624/1‑101 (MQ=9)
                                                                         aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  2:4410206/1‑101 (MQ=9)
                                                                         aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  2:667047/1‑101 (MQ=9)
                                                                         aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  1:108653/1‑101 (MQ=9)
                                                                          tCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAt  >  2:4333009/1‑101 (MQ=9)
                                                                                                    |                                                                              
TGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....C....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253790‑1253955

Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG