New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 392431 =41 (0.210)16 (0.080) 12/172 24.4 0.43 intergenic (‑79/+64) RCAP_rcc00363/trmD hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
?NC_014034 = 974293 1 (0.000)intergenic (+173/+86) RCAP_rcc00884/RCAP_rcc00885 hypothetical protein/hypothetical protein
Rejected: Position hash score below cutoff.

CTTTTGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCTCCCACAAATCCGGCC  >  NC_014034/392331‑392526
                                                                                                     |                                                                                                   
cTTTTGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTc                                                                                                     <  2:476433/101‑1 (MQ=255)
cTTTTGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTc                                                                                                     <  1:4207900/101‑1 (MQ=255)
 ttttGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCa                                                                                                    >  2:949318/1‑101 (MQ=255)
 ttttGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCa                                                                                                    <  2:2437029/101‑1 (MQ=255)
 ttttGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCa                                                                                                    <  1:2889778/101‑1 (MQ=255)
   ttGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCaaa                                                                                                  <  2:2802089/101‑1 (MQ=255)
    tGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAat                                                                                                 >  2:254609/1‑101 (MQ=255)
     gATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAata                                                                                                >  1:2749708/1‑101 (MQ=255)
      aTCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAatat                                                                                               <  2:454972/101‑1 (MQ=255)
      aTCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAatat                                                                                               <  1:3011575/101‑1 (MQ=255)
       tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.c                                                                                             <  2:3580873/101‑1 (MQ=255)
       tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.c                                                                                             <  2:2671946/101‑1 (MQ=255)
       tCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.c                                                                                             <  2:1462693/101‑1 (MQ=255)
         cGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.ccc                                                                                           <  1:3472534/101‑1 (MQ=255)
         cGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.ccc                                                                                           <  1:3152069/101‑1 (MQ=255)
          ggggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCg                                                                                          >  2:4295301/1‑101 (MQ=255)
           gggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgg                                                                                         <  2:220138/101‑1 (MQ=255)
           gggACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgg                                                                                         >  1:179888/1‑101 (MQ=255)
             gACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgggg                                                                                       <  2:177574/101‑1 (MQ=255)
             gACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgggg                                                                                       <  1:2648229/101‑1 (MQ=255)
             gACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgggg                                                                                       <  1:3542409/101‑1 (MQ=255)
               gatctaTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGt                                                                                     <  1:116895/96‑1 (MQ=255)
               cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCgggggc                                                                                     >  1:1665914/1‑100 (MQ=255)
               cGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGt                                                                                     <  1:4167715/101‑1 (MQ=255)
               atctcATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGt                                                                                     <  1:27688/97‑1 (MQ=255)
                ggCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTc                                                                                    <  1:1582609/101‑1 (MQ=255)
                ggCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTc                                                                                    <  1:480607/101‑1 (MQ=255)
                ggCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTc                                                                                    <  1:4059178/101‑1 (MQ=255)
                ggCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTc                                                                                    >  2:866014/1‑101 (MQ=255)
                 gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTcc                                                                                   <  1:3639235/101‑1 (MQ=255)
                 gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTcc                                                                                   <  2:3754313/101‑1 (MQ=255)
                 gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTcc                                                                                   <  2:692344/101‑1 (MQ=255)
                  ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.g                                                                                 >  1:3580170/1‑101 (MQ=255)
                   cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGtagat                                                                                 >  2:27675/1‑97 (MQ=255)
                   cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGGCC.gg                                                                                >  2:1158819/1‑101 (MQ=255)
                    aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGtagatc                                                                                >  2:116874/1‑96 (MQ=255)
                    aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.ggg                                                                               <  1:1285215/101‑1 (MQ=255)
                    aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.ggg                                                                               <  2:327110/101‑1 (MQ=255)
                     tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGTGGGTCC.gggg                                                                              >  1:2198585/1‑101 (MQ=255)
                      cgtaaaTCCCTCCTTGTCACCGCGGAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCCTGCCTCAAATAT.CCCGGGGGTCC.ggggg                                                                             <  2:2654214/98‑1 (MQ=255)
                      cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCG.TCTTGCCTCAAATAT.CCCGGGGGTCC.ggggg                                                                             >  2:1007048/1‑101 (MQ=255)
                      cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.ggggg                                                                             <  2:2747451/101‑1 (MQ=255)
                      cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.ggggg                                                                             <  2:1753668/101‑1 (MQ=255)
                       ggAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGc                                                                            >  1:3045692/1‑101 (MQ=255)
                        gAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCg                                                                           >  1:2451316/1‑101 (MQ=255)
                          aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGa                                                                         <  2:4169412/101‑1 (MQ=255)
                              cctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGccc                                                                     >  1:2287841/1‑101 (MQ=255)
                               ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGcccc                                                                    >  1:2945448/1‑101 (MQ=255)
                                   ttGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCcggc                                                                >  2:705057/1‑101 (MQ=255)
                                     gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCcggcgg                                                              >  1:634054/1‑101 (MQ=255)
                                     gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCcggcgg                                                              >  1:3116561/1‑101 (MQ=255)
                                       cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCgggg                                                            >  1:2018697/1‑100 (MQ=255)
                                             gcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGACTCAAATAT.CCCGGGGGTCC.CGGGGCGGAGCCCCCGGCGGGGCgagtt                                                      >  2:683634/1‑97 (MQ=25)
                                              ggagtctgcgCGGCCAAAGCGGGGGGGACAGTGCCAGCCTATTTCA.CCTACCCTTAAATCC.CCCGGGGGGCG.GGGGGCGGGCCCCCCGGCGGGTCGCCTCg                                                     <  2:2054715/92‑1 (MQ=255)
                                               aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCgggggggcgcgg                                                    >  1:3204842/1‑92 (MQ=255)
                                               aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGCAC.GGGGGGGGAGCCCCCGGCGGGGCgtggcgg                                                    >  1:3273239/1‑95 (MQ=37)
                                                aGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCgggggggcccggg                                                   >  1:2324663/1‑91 (MQ=255)
                                                    ctggCGGCCCAAACCGGGGGGAAAATGGCAGGCCATTTTC.TCTTGCC.CAAAAATCCCCGGGGGGCCGGGGGGGGGACCCCCCGGCGGGTCGCCTCGGCGCa                                                <  2:534198/98‑1 (MQ=16)
                                                     tggagccaaaaaCCGGGGGGACACGGGCCGGCTATTTCG.TCTTCCCTCAAAAGC.CCGGGGGGCCC.GGGGGCGCCCCCCCCGGCGGGTCGCCTCGGCGCAGc                                              <  1:1321046/92‑1 (MQ=12)
                                                             ccaaCCGGGGGGGCAACGTGCGGCCCTTTTATTCTTGCCTAAAATGC.CCGGGGGGTCG.GGGGGGAGGCCCCCCGGCGGGTCGCCTCGGCGCAGCCG.AGGCg                                      <  2:2945227/99‑1 (MQ=9)
                                                                                                tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCGGGGGGCCCCCGCGCCGGCC.GCGCGGAAACACCTGTCG.AACCTCCCCCCCACAACCCgcc  >  2:2886642/1‑101 (MQ=2)
                                                                                                tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCGGGGCGGCCCCGCGCCGCCGCGGGGGAAAACCCTTCCCGCAACTTCCCCCCCaacccagc    >  2:2883971/1‑95 (MQ=2)
                                                                                                     |                                                                                                   
CTTTTGATCCGGGGACGGCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCCGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCTCCCACAAATCCGGCC  >  NC_014034/392331‑392526

Base quality scores:  ATCG  < 3 ≤  ATCG  < 23 ≤  ATCG  < 30 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG