New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 392436 =45 (0.240)33 (0.180) 24/174 15.7 0.46 intergenic (‑84/+59) RCAP_rcc00363/trmD hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
?NC_014034 = 2330277 32 (0.150)intergenic (+252/+60) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GGCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330177‑2330373
                                                                                                    |                                                                                                              
gcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAg                                                                                                                <  1:3533946/99‑1 (MQ=255)
 cccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGa                                                                                                               >  2:49183/2‑101 (MQ=255)
  ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt                                                                                                              <  1:1731032/101‑1 (MQ=255)
   cccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtc                                                                                                             <  1:924742/101‑1 (MQ=255)
    ccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcc                                                                                                            <  1:3908986/101‑1 (MQ=255)
     cGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtccc                                                                                                           >  2:205535/1‑101 (MQ=255)
       cACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgg                                                                                                         >  2:714122/1‑101 (MQ=255)
        aCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccggg                                                                                                        >  1:3997206/1‑101 (MQ=255)
        aCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccggg                                                                                                        >  2:3403283/1‑101 (MQ=255)
           cccGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggt                                                                                                     <  2:118395/101‑1 (MQ=255)
             cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  2:3996946/101‑1 (MQ=255)
             cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  1:62403/101‑1 (MQ=255)
              ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                                  <  1:3684590/101‑2 (MQ=255)
               gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGatcccggggg.cccgg                                                                                                >  1:859780/1‑101 (MQ=255)
               gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  1:1644508/101‑3 (MQ=255)
               gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  2:2412673/101‑3 (MQ=255)
                cGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggg                                                                                                >  2:75346/1‑101 (MQ=255)
                 gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               <  1:3052015/101‑1 (MQ=255)
                 gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:2263649/1‑101 (MQ=255)
                 gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:496104/1‑101 (MQ=255)
                  tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            >  1:1901/1‑101 (MQ=255)
                  tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            <  1:714198/101‑1 (MQ=255)
                    tttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcg                                                                                          >  1:374631/1‑99 (MQ=255)
                      tGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcgga                                                                                        <  2:2991344/101‑5 (MQ=255)
                         gcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcc                                                                                     <  2:122333/101‑8 (MQ=255)
                         gcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcc                                                                                     <  1:2551832/101‑8 (MQ=255)
                           cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcccc                                                                                   >  2:957855/1‑92 (MQ=38)
                           cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcccc                                                                                   >  1:1322437/1‑92 (MQ=38)
                           cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G.....cggagcccc                                                                         <  1:75361/101‑9 (MQ=38)
                            aaGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagccccc                                                                                  >  1:815853/1‑91 (MQ=38)
                             aGAAAACGCCGGGGCGCGCGTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGTCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G.....cggagcccccg                                                                       <  1:1102860/101‑11 (MQ=25)
                                     ccGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCg                                                                   <  1:1947808/101‑1 (MQ=25)
                                       ggggCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGcc                                                                 >  1:2556730/1‑101 (MQ=25)
                                          gcgggcATGCGGGGCCCCGGAGCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAg                                                              <  1:633093/101‑1 (MQ=18)
                                          gcgcgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAg                                                              <  2:1812091/101‑1 (MQ=25)
                                            gcgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGc                                                            <  2:2760031/101‑1 (MQ=25)
                                             cgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGCGGcc                                                           >  2:257504/1‑100 (MQ=21)
                                               cATGCGGGGCCCGGGATCCCCGGCGGCCGGGGCGGCTTTCACCGGGGGCAAAAGATCCCGGGGGTCCGGGG..GGGGAG.....CCCCCGGC.GGGTCGCCGAGGCATc                                                         <  2:2188654/101‑1 (MQ=18)
                                                aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTGGcccgggcgggc                                                        >  1:358864/1‑92 (MQ=18)
                                                aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGGGCCGCGGGATCg                                                        >  1:1809229/1‑101 (MQ=21)
                                                  gCGGGGCCCCGGATCCCCGGCGGCCGGGGCGGCTTTCACCGGGGGCCAAAGACCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGcc                                                      <  2:2556539/101‑1 (MQ=18)
                                                    ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTc                                                    <  2:261005/101‑1 (MQ=25)
                                                    ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGGGCCGCGGCGTCGcccc                                                    >  1:617489/1‑99 (MQ=18)
                                                        ccccGGATCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.g                                              <  2:3004245/101‑1 (MQ=21)
                                                            ggATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAAt                                          <  2:3473194/101‑1 (MQ=25)
                                                                cACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGGGCGCCTCG.GC.GAGAAcccc                                      >  2:3928336/1‑100 (MQ=12)
                                                                 ccgggcggcCGGGGCGTCTTCCCCGGGGGGCAAAAGCCCCGGGGGGTCCGGGGGCG....GCC...CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCtt                                     <  2:1809110/98‑1 (MQ=9)
                                                                 ccgggcggcCGGGGCGGTTTCCACCGGGGGCAAAAGACCCGGGGGGCCGGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCtt                                     <  1:1485843/98‑1 (MQ=12)
                                                                   cggcggCCCGGGCGGTTTCCCCCGGGGGCCAAAGA.CCCGGGGGGCCCGGG..G....GCGGGCCCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAg                                   <  1:3568247/101‑1 (MQ=16)
                                                                    ggcggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCCGGGCAGCGCCGCC.GCGGAAAACCCtttg                                   >  2:1297074/1‑99 (MQ=9)
                                                                      cggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCGGCGCCCCGCCC.GAAACCCCttctaa                                 >  1:4125875/1‑97 (MQ=9)
                                                                       ggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGAGGGACCGCCCCT.GC.GCAAACCCCTTGTaaa                               >  2:3225069/1‑101 (MQ=9)
                                                                       ggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCCCGGCCGCCCCCCG.GC.CGAAACCCCTAGTaaa                               >  1:3929461/1‑101 (MQ=2)
                                                                          ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGACGGATCCCCCCG.GCGGAAAACCCtacgaaaaca                             >  2:4217125/1‑92 (MQ=9)
                                                                           cGGGCGGCTTTCCCCGGGGCCCAAAGTCCCGGGGGGTCCGGGG..GGGGCG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAcc                           <  2:374580/101‑1 (MQ=16)
                                                                           cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAcc                           <  2:3459546/101‑1 (MQ=25)
                                                                            gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGCGGCAACGCCCCG.GG.GAAAACCCCTatgaaaaacac                          >  2:3891299/1‑91 (MQ=9)
                                                                              gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGGTCGCCCCC.GC.GGCAACCCTTTGTAAAAAccgcc                        >  1:1889128/1‑101 (MQ=9)
                                                                                ggcTTCCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAccgcccg                      <  2:3780415/101‑1 (MQ=21)
                                                                                 gcTTTCACCGGGGGCCAAAGACCCCGGGGGTCGGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAccgcccgc                     <  2:3005977/101‑1 (MQ=21)
                                                                                  cTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGATCGCCCCC.GCGGAAAACCCTT.GTAAAAACCCCCcccg                    >  1:1474315/1‑101 (MQ=2)
                                                                                   tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGGCGAGGGGTCGCCCCC.GC.GGAATCCCCCATTAAAAAACGCCCCCgg                   >  1:792814/1‑101 (MQ=2)
                                                                                   tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGATCGCCCCG.GC.GAAAACCCCTAGTAAAAAacgccccccg                   >  1:2307711/1‑97 (MQ=9)
                                                                                     tCACCTGGGGCCAAAGAGCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGAc                 <  2:2454810/101‑1 (MQ=21)
                                                                                         cTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCCCCGCCTCC.GC.GAAATCCCCTTTTAAAAAACCCCCGCCGCCAggg             >  1:1403811/1‑101 (MQ=0)
                                                                                          tGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGGCGCC.AGGCCGCGCCCCC.GC.GCAAACCCTTCCTTAAAAACGCCCCCGGGCAGGGa            >  1:557496/1‑101 (MQ=2)
                                                                                               ccAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGa       <  2:1522890/101‑1 (MQ=21)
                                                                                                    gATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCATCGCCTCG.GC.GAAAACCCTTAGTAAAAACCGCCCGCGGGCAGGGGGCCGAAgggc  >  2:183346/1‑99 (MQ=12)
                                                                                                    |                                                                                                              
GGCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330177‑2330373

Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG