New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 392448 =50 (0.220)21 (0.090) 8/190 26.2 0.28 intergenic (‑96/+47) RCAP_rcc00363/trmD hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
?NC_014034 2330184 = 60 (0.250)intergenic (+159/+153) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTC  >  NC_014034/392348‑392548
                                                                                                     |                                                                                                      
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGNNnc                                                                                                        <  2:2637226/101‑1 (MQ=255)
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTcc                                                                                                        <  1:100751/101‑1 (MQ=255)
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTcc                                                                                                        <  2:1013038/101‑1 (MQ=255)
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTcc                                                                                                        <  2:2642880/101‑1 (MQ=255)
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTcc                                                                                                        >  2:3762773/1‑101 (MQ=255)
 ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.g                                                                                                      >  2:4159264/1‑101 (MQ=255)
 ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.g                                                                                                      <  2:3831499/101‑1 (MQ=255)
 ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACGATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.g                                                                                                      <  1:1154841/101‑1 (MQ=255)
  cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.gg                                                                                                     <  2:558431/101‑1 (MQ=255)
   aTCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.ggg                                                                                                    >  2:3245738/1‑101 (MQ=255)
    tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.gggg                                                                                                   >  2:2284175/1‑101 (MQ=255)
    tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.gggg                                                                                                   <  2:4683642/101‑1 (MQ=255)
     cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.ggggg                                                                                                  >  1:4120086/1‑101 (MQ=255)
      ggAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGc                                                                                                 >  1:3568035/1‑101 (MQ=255)
      ggAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGc                                                                                                 <  2:4179527/101‑1 (MQ=255)
      ggAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGc                                                                                                 <  1:2066446/101‑1 (MQ=255)
        aaaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCgg                                                                                               >  2:2763148/1‑101 (MQ=255)
         aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGa                                                                                              <  2:4335838/101‑1 (MQ=255)
          aTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAg                                                                                             >  1:3592547/1‑101 (MQ=255)
          aTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAg                                                                                             <  1:1732156/101‑1 (MQ=255)
            cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGcc                                                                                           <  2:1730266/101‑1 (MQ=255)
             cctcctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGccc                                                                                          >  1:4576946/1‑101 (MQ=255)
               tcctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGccccc                                                                                        >  2:2148173/1‑101 (MQ=255)
               tcctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGccccc                                                                                        >  2:1086710/1‑101 (MQ=255)
               ccctttcccccGCGCAAGCCTATGCGCCCAAAC.CCGGAGGGACAAGGGCAGCCCATTTCATTTTCCCTCAAATACCCCGGGGGTCC.GGGGGCGGACccccc                                                                                        <  2:1953036/92‑1 (MQ=16)
                cctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCc.g                                                                                      >  1:2718381/1‑101 (MQ=255)
                cctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCc.g                                                                                      >  1:1300299/1‑101 (MQ=255)
                 ctTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCc.gg                                                                                     >  1:2177824/1‑101 (MQ=255)
                   tGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCc.ggcg                                                                                   >  2:701085/1‑101 (MQ=255)
                    gTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCc.ggcgg                                                                                  >  1:1895420/1‑101 (MQ=255)
                     tCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCggg                                                                                 >  2:1260483/1‑101 (MQ=255)
                     tCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCggg                                                                                 >  1:4280120/1‑101 (MQ=255)
                       aCCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGGGCCCCC.GGCggggg                                                                               >  1:2069655/1‑99 (MQ=255)
                        ccGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCgggggg                                                                              >  1:3542365/1‑98 (MQ=255)
                        ccGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCAGTTCATCTTGCTAAAAAGATACCGTTGGGCC.GGAGGCGGTGCCCGC.GGCGGGGCg                                                                              >  2:1103533/1‑101 (MQ=255)
                            gaaaGACTATG.GGCCCAAAGCGGGGGGGAAAAGGGCGGCCCTTTTCATCTTCCCTCAAATACCCGGGGGGTCG.GGGGGGGGACCCCCC.GGCGGGTCGCCTc                                                                          <  2:4690913/99‑1 (MQ=9)
                             cAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCgggggggcccg                                                                         >  1:4531580/1‑93 (MQ=255)
                             cAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCggggggcggcg                                                                         >  2:2493430/1‑93 (MQ=255)
                              aaGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCgggggggccccc                                                                        >  2:10617/1‑92 (MQ=255)
                              aaGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCggggggcgtccg                                                                        >  2:2287003/1‑92 (MQ=255)
                                  cTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCTCGGGGCa                                                                    >  1:3913598/1‑101 (MQ=255)
                                   tATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCGCCgcgggg                                                                   >  1:1450434/1‑98 (MQ=21)
                                    aTGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGGCCCGgcggcgc                                                                  >  2:1353985/1‑97 (MQ=21)
                                        ggCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCCgcggccgccgc                                                              >  1:1411890/1‑93 (MQ=18)
                                           ccAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGGCCCGgcgccggccgcgcg                                                           >  2:2236432/1‑91 (MQ=21)
                                                     ggggACAAGGGCAGCCCTTTCCATCTTCCCAAAAATACCCGGGGGGCCG.GGGGGCGGCCCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACtt                                                  <  2:4576693/100‑1 (MQ=16)
                                                                ggggctttttCTTCTT.CCCCAAATACCGCGGGGGTGC.GGGGGGGGAGCCCCCGGGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTtct                                       <  2:2106137/94‑1 (MQ=21)
                                                                  ggCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGGGCGGCCCGGGGGAAAAAACATTCCGCACATCTcc                                     >  2:1053359/1‑101 (MQ=9)
                                                                          cATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGGCTCCGCGCGGCCGGGGCGGAAAAACTTGCCGGACCTTTccccccaaca                             >  1:1344456/1‑94 (MQ=9)
                                                                          cATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCCGCGCCGCCCGGGGGGAAACACCTGCCGGACCTCCccccccaacc                             >  2:1626533/1‑94 (MQ=2)
                                                                           ctttttccTCAAAATCCCCGGGGGGCCGGGGGGGGGCCCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATc                             <  1:2148297/95‑1 (MQ=21)
                                                                            tCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGCCCCCGCGCGGGCGGGGGGGAAACAATTTCCGAACCTCTCCcacccaaccc                           >  2:2159204/1‑94 (MQ=9)
                                                                             cTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGGCTCGGCGCCGCCGGGGGGGAAACACCTTCCGCACATCTcccccccaccccc                          >  2:4209365/1‑91 (MQ=9)
                                                                             cTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGGCCCCGCGCCGCCGCGGCGGAAACACATTCCCCACTTCTcccccccaacccc                          >  1:78433/1‑91 (MQ=9)
                                                                                     aaactcccggggggTCC.GGGGGCGCGCCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATCCGGCCGCCGGt                  <  2:583615/92‑1 (MQ=25)
                                                                                      aaTATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCGGCGCCGCCCAGGCGGAAACACTTGCCCGACCTCTCCCCCCAAACCCgccccccgcc                 >  2:3598708/1‑97 (MQ=9)
                                                                                       atatCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGGGGCGCGGGGCAGCCGGGGCGGAAACAATTTTCGCACTTCTCCCACAAACACCGCCCCCGGCcc                >  2:2825615/1‑101 (MQ=9)
                                                                                         cccccGGGGGGCGGGGGGGCGCACCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATCCGGCCGCCGGTccc               <  2:3886075/99‑1 (MQ=25)
                                                                                           cccGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCCGCGCCGGCGCGGCGGAAACACCTTCCGAACATCTCCCCCCAAACCCCCCGCCCGGcccccc            >  1:383938/1‑98 (MQ=9)
                                                                                            ccGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCGGCGCCGCCGAGGGGGAAACACCTGCCGCACTTCTCCCCCAAATCCGGCCCCCGGGCCcgcgc           >  2:2597637/1‑100 (MQ=21)
                                                                                             cGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCCCGGCGCCGCCACGGCGCGAACACCTGTCGCACCTCTCCCCCAAAACCACCGCCCCGTCCcgccgc          >  2:2345944/1‑98 (MQ=2)
                                                                                              gggggTCC.GGGGGCGGAGCCCCC.GGCGGGGCGCCTCCGCGCCGCCGGCGCGGAAACACCTTCCGACCTTTTCCCCCCAAACCCCCCGCCCGGCCCGCGCCa         >  2:2807399/1‑101 (MQ=9)
                                                                                                     c.GGGGGCGGCGCCCCG.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTc  <  2:1540049/101‑1 (MQ=255)
                                                                                                     |                                                                                                      
GCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAA.CCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTCTCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTC  >  NC_014034/392348‑392548

Base quality scores:  ATCG  < 3 ≤  ATCG  < 24 ≤  ATCG  < 31 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG