New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 392448 =52 (0.230)15 (0.070) 5/190 34.3 0.24 intergenic (‑96/+47) RCAP_rcc00363/trmD hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
?NC_014034 2330184 = 42 (0.180)intergenic (+159/+153) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTCCCGCGTCAAAGCTT  >  NC_014034/392348‑392547
                                                                                                     |                                                                                                        
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTc.c                                                                                                          <  1:3035484/101‑1 (MQ=255)
gCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTc.c                                                                                                          >  2:4487244/1‑101 (MQ=255)
 ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cg                                                                                                         >  1:446198/1‑101 (MQ=255)
 ccATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cg                                                                                                         <  2:574377/101‑1 (MQ=255)
  cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgg                                                                                                        <  2:2646828/101‑1 (MQ=255)
  cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgg                                                                                                        >  1:1019014/1‑101 (MQ=255)
  cATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgg                                                                                                        >  1:1763019/1‑101 (MQ=255)
    tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                                      <  2:3137630/101‑1 (MQ=255)
    tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                                      <  2:3216399/101‑1 (MQ=255)
    tCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cgggg                                                                                                      <  1:2355757/101‑1 (MQ=255)
     cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggggg                                                                                                     >  1:2693504/1‑101 (MQ=255)
     cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggggg                                                                                                     <  1:2897860/101‑1 (MQ=255)
     cGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggggg                                                                                                     <  1:4361389/101‑1 (MQ=255)
      ggAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGc                                                                                                    <  2:4667882/101‑1 (MQ=255)
       ttccgatctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCg                                                                                                   <  2:638235/94‑1 (MQ=255)
       gAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCTGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGGC.CGGGGGCg                                                                                                   >  2:2993743/1‑101 (MQ=255)
       gAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.Cggggggg                                                                                                   >  2:435831/1‑99 (MQ=255)
       gAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCg                                                                                                   >  1:2472620/1‑101 (MQ=255)
       gAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCg                                                                                                   >  1:2414522/1‑101 (MQ=255)
        aaaGCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCgg                                                                                                  <  2:328145/101‑1 (MQ=255)
         aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGa                                                                                                 <  1:3559480/101‑1 (MQ=255)
         aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGa                                                                                                 >  2:1822315/1‑101 (MQ=255)
         aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGa                                                                                                 <  1:4119902/101‑1 (MQ=255)
         aaTCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGa                                                                                                 <  1:937674/101‑1 (MQ=255)
          aTCCCTCCTTGGCCCCGCCAAAGGCCAGGCGGCCCAAAACGGAGGTACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGATGGAg                                                                                                <  2:1246081/101‑1 (MQ=21)
           tCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGc                                                                                               >  1:830202/1‑101 (MQ=255)
            cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcc                                                                                              <  2:4652593/101‑1 (MQ=255)
            cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcc                                                                                              <  2:4225515/101‑1 (MQ=255)
            cccTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcc                                                                                              >  1:308842/1‑101 (MQ=255)
             cctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGccc                                                                                             <  2:3570361/101‑1 (MQ=255)
             cctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGccc                                                                                             >  2:1965786/1‑101 (MQ=255)
              ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                                            <  1:1913759/101‑1 (MQ=255)
               tcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATTCCGGGGGTC.CGGGGGCGGAGccccc                                                                                           >  2:4345039/1‑101 (MQ=255)
               ccctTGCCACCGCGCAAGACTAGGCGGCCAAAACCGGAGGGAAAAGGGCAGGCCATTTCATCTTGCCTAAAATACCCGGGGGGCC.GGGGGGGGGACccccc                                                                                           <  2:3883475/100‑1 (MQ=255)
                cctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCgagatcggaa                                                                                          >  1:638296/1‑92 (MQ=255)
                 ctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc.gg                                                                                        >  1:3867400/1‑101 (MQ=255)
                   tGTAACCGCGCAAGCCTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTAATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGGGCCCCc.ggcg                                                                                      >  2:4633304/1‑101 (MQ=37)
                    gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc.ggcgg                                                                                     >  2:3726055/1‑101 (MQ=255)
                     tCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCggg                                                                                    >  2:2232111/1‑101 (MQ=255)
                      cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggg                                                                                   >  2:1271841/1‑100 (MQ=255)
                       aCCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCggggg                                                                                  >  1:308611/1‑99 (MQ=255)
                        ccGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggggg                                                                                 >  1:1213021/1‑98 (MQ=255)
                              aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggggggcggtg                                                                           >  2:85766/1‑92 (MQ=255)
                                        ggCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGCGGCCCGGGG.CCGccccg                                                                >  1:2819665/1‑98 (MQ=21)
                                             aaaCCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.GCGCCGCGGCgga                                                           >  2:4451234/1‑99 (MQ=18)
                                                      ggaacagggCCGGCCCTTTCCTTTTTCCCAAAACTTCCCGGGGGGCGGGGGGGGGGCCCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTg                                                  <  2:2648149/94‑1 (MQ=9)
                                                           aTGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCCGCG.CCGGCGAGGGGGAAACA.catacccaaa                                            >  2:3105023/1‑92 (MQ=14)
                                                                    cATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCTCGGCG.CCGCCCAGGCGGAAAAA.CATTCCCGACTTCT.ccccc                                  >  2:2872107/1‑99 (MQ=17)
                                                                                 cTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCTCGGCG.CCGCCGGGGGGGAAAAA.CTTTCCGCACCTCT.CCCCCCCACCCCgccg.cc                    >  2:3434921/1‑101 (MQ=9)
                                                                                  tCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.GGGGCGCGGCGGAAACACCTTCCCGACCTTTC.CCCCCAAACCCGcccc.cc                    >  1:3489145/1‑101 (MQ=2)
                                                                                      atatCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGCG.CGGCCGCGGGGGAAACA.CTTTCCCAACCTCT.CCCCCCAAACCCGCCC.CCGGCcc               >  1:514642/1‑101 (MQ=9)
                                                                                       atccccGGGGGGC.CGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTcc               <  1:2013339/98‑1 (MQ=37)
                                                                                       acccgggggggCC.GGGGGGCGGGCCCCCCGGGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTcc               <  1:2004951/95‑1 (MQ=25)
                                                                                          cgggggggGC.GGGGGGGGGGCCCCCC.GGCGGGGCGCCGCGGCG.CACCCGAGGCGAAATCC.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTCCcgcg           <  1:656657/98‑1 (MQ=255)
                                                                                             tctggTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTCCCGCGTCa        <  2:2196329/98‑1 (MQ=255)
                                                                                             gggggTC.CGGGGGCGGAGCCCCC.GGCGGGGCGCCCCCGCG.CCGCCCGGGGGGAAACA.CTTGCCGAACCTCTCCCCCCAAACCCGCCCC.CCGGCcccccccc         >  1:3024107/1‑96 (MQ=9)
                                                                                              gcgggggcGGGGGCGGCCCGCCG.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTCCT.CCCACAAATCCGGCCG.CCGGTCCCGCGTCa        <  1:4364068/94‑1 (MQ=25)
                                                                                               gggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGGG.CGGCCCCGGGGGGAACA.CCTTCCGGACCTCT.CCCCCACAACCGGCCC.CCGGCGCcgccgccca      >  1:4631728/1‑95 (MQ=2)
                                                                                               gggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.CCGCCGGGGGGGAAAAA.CTTGCCGCACTTCT.CCCCCAAAACCCGCCG.CCCGGCCCGCGCCaaa      >  2:3098596/1‑101 (MQ=16)
                                                                                                ggTC.CGGGGGCGGAGCCCCC.GGCGGGGTGGCCCGGGG.CACGCGCGGCGCAAACA.ATTGCCCACCCGCT.CCCCCCAATACCGCCG.CCGGTCCCCCGCCCAAg     >  1:4446381/1‑101 (MQ=2)
                                                                                                ggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGGG.CCGCCCCGGGGGAAACA.CCTGCCCAACTTCT.CCCCCCAAACCCGCCG.CCCGGccccccgccaca     >  1:2196479/1‑92 (MQ=9)
                                                                                                  tC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGCGCCGGCCGGGGGGAAACAA.CTT.CCGCACTTCT.CCCCCCAAACCGCCCG.CCCGGCCcgccgccaaacc   >  2:3357613/1‑92 (MQ=255)
                                                                                                   c.cGGGGGCGGAGCCCCC.GGCGGGGGGCCCCCGCG.CCGCCCCGGCGGAAACA.CCTGCCGAAACTCT.CCCCCAAAACCCGCCGCCCGGTCCC.CGCCAAAggct  >  2:3086984/1‑98 (MQ=255)
                                                                                                     |                                                                                                        
GCCATCGGAAATCCCTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGGCCG.CCGGTCCCGCGTCAAAGCTT  >  NC_014034/392348‑392547

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 28 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG