New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 744655 =63 (0.300)36 (0.170) 13/196 23.3 0.42 intergenic (+40/+172) idi2/bchO isopentenyl‑diphosphate delta‑isomerase/magnesium‑chelatase BchO
?NC_014034 1253897 = 35 (0.170)intergenic (+55/+36) RCAP_rcc01181/hisH hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTGGCTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTG  >  NC_014034/744555‑744755
                                                                                                      |                                                                                                       
cTGGCTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCCTGCGCCTCGGGCGACccg.cc                                                                                                         >  2:183811/1‑101 (MQ=255)
  gccTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTGCGGCGGGTGACGGCC.TGAGATTTCGCCGGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..gg                                                                                                     <  2:2639892/99‑1 (MQ=255)
   gCTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGGGCTTGCGCCTCGGGCGACccg.ccccc                                                                                                      >  1:3550603/1‑98 (MQ=255)
    cTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACccg.cccccc                                                                                                     >  1:1523629/1‑97 (MQ=255)
    cTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..gggg                                                                                                   >  2:536255/1‑101 (MQ=255)
     tCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..ggggg                                                                                                  >  1:3922270/1‑101 (MQ=255)
     tCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..ggggg                                                                                                  >  1:657363/1‑101 (MQ=255)
       aaGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCGGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCt                                                                                                <  1:3844779/101‑1 (MQ=255)
        ataTCTATATCGAGCAGCACCGCGACATTATCTTTCCGCCGGTGACGGCC.TGAGATTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTc                                                                                               <  2:3421369/99‑1 (MQ=255)
         gATCTATATCGAGCAGCACCGCGACATGATCTTCCCGCCGGTGACGGCC.TGAGATTTCGCCGGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTcc                                                                                              <  1:2085932/101‑1 (MQ=255)
            cTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTNCGCCTCGGGCGACCCG.CC..cgggggggcgcc                                                                                           >  1:1518987/1‑94 (MQ=255)
            cTATACCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGCCGCGTTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.cc                                                                                          <  2:1082546/101‑1 (MQ=255)
             tataTCGAGCAGCACCGCGACATTATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGGTCCG.tcc                                                                                         >  2:727772/1‑101 (MQ=255)
              atatCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..CGGGGGGCCG.cccc                                                                                        >  1:1603767/1‑101 (MQ=255)
              atatCGAGCAGCACCGCGACATGATCTTCCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.cccc                                                                                        <  2:2372365/101‑1 (MQ=255)
              agatCGAGCCGCACCGCGACAGGATCTTGCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCCCCGGGGGCGCCCCG.CC..GGGGGCTCCG.cccc                                                                                        <  2:308624/99‑1 (MQ=37)
                atCGAGCAGCACCGCGACATGATCTTTCCGCCGGGGACGGCC.TGAGATTCCGCCCGGGGCGCGCTTGCGCCTGGGGCGACCCG.CC..GGGGGCTCCG.CCCCCg                                                                                      <  2:3913909/101‑1 (MQ=255)
                agggAGCAGCCCCGCGACATGATCTTTCCGCGGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCg                                                                                      <  2:1284313/98‑1 (MQ=255)
                 tggAGCAGCCCCGCGAAATGATCTTCCCGCCGGTGAGGGCC.TGAGATTTCGCCCGGGGCGCGCTGGCGCCCCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCgg                                                                                     <  2:2584544/99‑1 (MQ=37)
                 tggAGCAGCACCGCGACATGATCTTCCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTGGGGCGACCCG.CC..GGGGGCTCCG.CCCCCgg                                                                                     <  2:1960145/99‑1 (MQ=255)
                 ccGACCAGCACCGCGACAGGTTCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGTTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCgg                                                                                     <  2:1299967/100‑1 (MQ=38)
                   gaccacccccGCGACTTGATCTTCCCGCGGGTGCCGGCC.TGAGTTTCCGCCGGGGGCGCGCTTGCGCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGAc                                                                                   <  2:3165764/93‑1 (MQ=18)
                   gAGCAGCCCCGCGACATGATTTTTCCGCCGGGGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGAc                                                                                   <  2:1240210/101‑1 (MQ=38)
                   gAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..CGGGGGGCCC.ccccccccc                                                                                   >  1:1729709/1‑97 (MQ=255)
                       agcccggcgACATGATCTTCCCGCCGGTGCCGGCC.GGAGTTTTCGCCCGGGGCGCGTTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGAccccc                                                                               <  2:1530066/95‑1 (MQ=25)
                       agccCCGGGACATGATCTTCCCGCCGGTGCCGGCC.TGAGATTCCGCCGGGGGCGCGCTTGCGCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGAccccc                                                                               <  1:532741/101‑1 (MQ=21)
                       acccccGCTAAATGATTTTTCCGCCGGTGCGGGCC.TGAGTTTTCGCCCGGGGCGCGTTTGCGCCTGGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGAccccc                                                                               <  2:2540320/97‑1 (MQ=21)
                         ccccGCGACAGGTTCTTCCCGCCGGTGGCGGCC.TGGGATTTCGCCGGGGGCGCGCTGGCGCCGGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCgg                                                                             <  1:574524/99‑1 (MQ=21)
                          cccGCGACATGATCTTCCCGCGGGTGACGGCC.TGAGTTTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCggg                                                                            <  1:1293307/100‑1 (MQ=25)
                          cccGCGACATGATCTTCCCGCCGGTGCCGGCC.TGAGTTTCCGCCCGGGGCGCGCTTGCCCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCggg                                                                            <  1:3342379/100‑1 (MQ=37)
                             cggcatggcccTTCCCGCCGGTGACGCCC.GGACATTCCGCCCGGGGCGCGCTGGCGCCGCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGata                                                                         <  1:4232588/91‑1 (MQ=18)
                              cgACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCGCCC..GCGGGACCCC.CCCCCGGCccccccgccag                                                                         >  1:593753/1‑95 (MQ=255)
                              cgACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGGTCCGCCCCCCGGCCCCCCggggct                                                                         >  2:1831135/1‑98 (MQ=38)
                               gACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CCCGGGGGGCGCGC.CCCCCCGCCCCCCggggcg                                                                         >  1:271402/1‑98 (MQ=255)
                                 ctggttCTTCCCGCGGGTG.CGGCCGTGAGATTGCCCCGGGGGCGCGCTTGCCCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTg                                                                     <  1:2916727/96‑1 (MQ=12)
                                   tgttCTTCCCGCGGGTGCGGGCG.TGAGTTTCCGCCGGGGGCGCGCTTGCGCCGGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTggg                                                                   <  1:2934559/98‑1 (MQ=18)
                                      tctccccgcggGGGACGGCC.TGAGTTTCCGCCCGGGGCTCGCTTGCGCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCa                                                                <  1:579974/96‑1 (MQ=21)
                                      tctccccgccgGCGGCGCCT.GGAGTTTCCGCCGGGGGCGCCCTGGCGCCCGGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCa                                                                <  1:2105134/96‑1 (MQ=9)
                                        tttCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCCGGCCCCCGGGGTATTTGGGGGAAg                                                              >  2:1159268/1‑101 (MQ=37)
                                          tCCGCGGGGGAGGGCC.TGAATTTCCCCCCGGGGCCCGCTTCCGCCGCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGat                                                            <  2:3894313/101‑1 (MQ=17)
                                           ccggcgGTGACGGCC.GGGGTTTCCGCGCGGGGCGCGTTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGatg                                                           <  2:1517523/101‑1 (MQ=18)
                                           ccgccgGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCGCCC..GGGGGGCCCC.CCCCCCCCCCCCCGGGGGATTTtgggggagag                                                            >  1:2473119/1‑95 (MQ=255)
                                            cgccgTTGACGCCC.GGAGTTTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGatga                                                          <  2:2388024/101‑1 (MQ=21)
                                                ggggccGGCC.TGAGTTTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGatgaaatg                                                      <  1:2411677/96‑1 (MQ=21)
                                                ggTGCCGCCG.TGAGATTGCGCCGGGGGCGCGCTTGCCCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGatgaaatg                                                      <  2:3829964/101‑1 (MQ=18)
                                                 gTGCCGGCC.TGAGTTTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGatgaaatga                                                     <  1:183849/101‑1 (MQ=21)
                                                    gcGGCC.TGAGATTCCGCCGGGGGCGCGCTTGCGCCGCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAaatgaatg                                                  <  1:3389211/100‑1 (MQ=21)
                                                    aCGGCC.TGAGTTCGCGCCGGGGGCGCCCCCGCCCGGGGCGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAaatgaatg                                                  <  2:3550350/101‑1 (MQ=9)
                                                      ggCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CCG.GGGGGCCCCG.CCCCGGGCCCCCCGGG.GATTTGGGGCCAGatggaaaggattac                                                >  1:1235267/1‑93 (MQ=25)
                                                         ccggagtTTTCGCCGGGGGCGCGGTTGCCCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACtt                                              <  1:2383970/98‑1 (MQ=18)
                                                           tGAGTTTTCGCCGGGGGCGCGCTTGCGCCGCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTc                                            <  1:3031199/101‑1 (MQ=21)
                                                           tGAGTTTCCGCCGGGGGCGCGCTTGCGCCTCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTc                                            <  1:916986/101‑1 (MQ=21)
                                                           tGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGGTCCG.CCCCCCGACCCCCCGGGGATTTTGGGGAAGATGAAAAGAAAGAATTTc                                            >  2:3480757/1‑101 (MQ=21)
                                                                  tCGCCGGGGGCGCGCTTGCGCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTgc                                     <  2:3922010/101‑1 (MQ=255)
                                                                  ccGCCCGGGGCGCGCTGGCCCCGCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTgc                                     <  2:770957/100‑1 (MQ=255)
                                                                   cGCGCGGGGCGCGCTTGCCCCTGGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTgcg                                    <  1:3481009/101‑1 (MQ=21)
                                                                        ggggGGCGCTGGCCCCCGGGGCCTCCCG.CC..GGGGGCTCCT.CCCCCGGACCCCCGGGATATTGGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGt                               <  2:462184/101‑1 (MQ=18)
                                                                          ggccccctcgcgcCCCGGGCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTAc                             <  2:1523525/92‑1 (MQ=21)
                                                                           gccctctgccgcCTCGGGCCCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACa                            <  2:1518883/92‑1 (MQ=21)
                                                                                cTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTg                       <  1:1000198/101‑1 (MQ=255)
                                                                                 tgccgcCGCGGGCCCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGt                      <  2:258906/98‑1 (MQ=25)
                                                                                     cccgcGGCCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCa                  <  1:2623875/97‑1 (MQ=255)
                                                                                        tggggCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCAccc               <  2:3949053/99‑1 (MQ=255)
                                                                                           ggCGCCCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTg            <  1:1159362/101‑1 (MQ=255)
                                                                                            gccccccG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGc           <  2:3150801/97‑1 (MQ=255)
                                                                                             cGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTgat          <  1:785972/101‑3 (MQ=255)
                                                                                                      c..gGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTg  <  2:1235171/101‑1 (MQ=255)
                                                                                                      c..gGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTg  <  1:440705/101‑1 (MQ=255)
                                                                                                      c..gGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTg  >  1:2150029/1‑101 (MQ=255)
                                                                                                      c..gGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTg  <  2:824596/101‑1 (MQ=255)
                                                                                                      |                                                                                                       
CTGGCTCAAGATCTATATCGAGCAGCACCGCGACATGATCTTTCCGCCGGTGACGGCC.TGAGATTTCGCCCGGGGCGCGCTTGCGCCTCGGGCGACCCG.CC..GGGGGCTCCG.CCCCCGGACCCCCGGGATATTTGGGGCAAGATGAAATGAATGACTTTCCGTCTGCGGCGGTACAGCCTGTCCCACCCCTGCTTTTCCTTG  >  NC_014034/744555‑744755

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG