New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 125389037 (0.160)28 (0.120) 4/192 35.6 0.40 intergenic (+48/+43) RCAP_rcc01181/hisH hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
?NC_014034 = 1721531 48 (0.200)intergenic (‑426/+20) RCAP_rcc01588/RCAP_rcc01589 GSCFA family protein/ErfK/YbiS/YcfS/YnhG family protein
Rejected: Position hash score below cutoff.

GGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCC..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721443‑1721631
                                                                                            |                                                                                                    
ggCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCCGGGGGCTGCGCCCCCCGGcccccc                                                                                            >  2:4224993/1‑101 (MQ=25)
gccccccctcccGCTGCTTTTTTTTTTGGGCGGGTCGCGTGGGGGTTTC.CGCCGGGGCGGCGCGGGGG.CCCCCCGCCGGGGGCTGCGCCCCCGGAcccccc                                                                                            <  1:1542242/96‑1 (MQ=255)
     cccccccGCCGTGTTTTTTTTGTGGCGGGTCGCTTGGGGGTTTC.CGCCTCGGCGGCGCGGGGG.CGCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGaa                                                                                       <  2:3816818/101‑1 (MQ=9)
       ctcccGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCCGGGGGGGGCGCCCCCCGGcccccccccccaa                                                                                     >  2:557102/1‑96 (MQ=21)
           cGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCCGGGGGCTGCGCCCCCCGGccccccccccagaaccc                                                                                 >  1:1347017/1‑92 (MQ=18)
                ttttttTTTTTGGGCGGGTCGCGTGGGGGTTTC.CCCCCGGGCCGCCCCGAGG.CGCCCCGCCGGGGGCTGCGCCCCCGGA.CCCCCCCGAAGATCTCAGATCa                                                                           <  1:2732696/98‑1 (MQ=255)
                gtttttTTTTTTTGGCGGTCCCCGTGGGGGTTTCCGCCCCGGCGGCCCCGGGC.CCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGAt                                                                             <  2:3580995/98‑1 (MQ=255)
                 tttttTTTTTTGGCGGGTCGCCGGGGGGTTCC.CCCCCCGGCGCCCCCGAGG.CCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCa                                                                           <  1:370232/99‑1 (MQ=12)
                 gcTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACACGCCGGGGGGTGCGCCCCCGGAGCCCCCCCCAAGAACTCACATcc                                                                           >  2:4326990/1‑100 (MQ=18)
                     tttttttGGCCGGTCCCTGTGGGGTTTC.CGCCCCGGCGGCGCCGGGG.CGCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCtt                                                                       <  1:783133/99‑1 (MQ=255)
                     ttttttgGGGCGGGCGCCTTGGGGTTTTCCCCCGCGGCGCCGCCGGGG.CCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCt                                                                        <  1:3820537/99‑1 (MQ=12)
                       tttggggCCGGCCG.CTTGGGGTTTTCCCCCGCGGCGGCCCGGGGG.CCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGa                                                                     <  1:2495366/96‑1 (MQ=12)
                        ttttGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCCGGGGGCGGCGCCCCCGGACGCCCCCCCACAATCTCACGACACCCTGAc                                                                    >  2:1566460/1‑101 (MQ=17)
                            ggCCGGCGGGCTTGGGGGTTT.CGCCCCGGGGCCCCCGGGGCCCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTg                                                                 <  2:4586876/101‑1 (MQ=255)
                               cgggcgctggggggTTTT.CGCCGGGGCCGCCCCGGGC.CCCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTg                                                             <  1:2224337/91‑1 (MQ=255)
                                                t.CGCCTCGGCTGCGCCGAGG.CGACCCGCCGGGGGGTGCGCCCCCCGGCCCCCCCCCCAAAGCTCCGATACCCTTTACCCGCGCGCCGGCCCGGCCGAGCgg                                            >  2:2159063/1‑101 (MQ=2)
                                                       cGGCTGCGCCGAGG.CGACCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGCAGATCTCAGATCACCTTGACCCGCGTGCCGACCGGGCAGAGCGGACaaaa                                      >  2:1356187/1‑100 (MQ=25)
                                                           tGCGCCGAGG.CGACCCGCCGGGGGCTGCCCCCCCGGACCCCCCCCCACGATCTCAGATCCCCCTGACCTGCGCGCCGGCCGGGCAGAGCGGATAAAATTcc                                  >  2:1349236/1‑101 (MQ=21)
                                                                 gggg.CGCCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGAcc                            <  1:2551368/99‑1 (MQ=255)
                                                                             ccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGaa                 <  2:210489/97‑1 (MQ=255)
                                                                              cgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAAc                <  1:2451795/98‑1 (MQ=255)
                                                                              cgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAAc                <  1:2023027/98‑1 (MQ=255)
                                                                               gggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACa               <  2:2741868/99‑1 (MQ=255)
                                                                               gggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACa               <  1:1701439/99‑1 (MQ=255)
                                                                                ggggCTGCGCGCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGGGCGGACCCGGCAGAGCGGATAAAGTTCCTGGACCTGGGCATCGAACAg              >  2:1529576/2‑101 (MQ=255)
                                                                                ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              >  1:3569715/2‑101 (MQ=255)
                                                                                ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              <  1:24884/100‑1 (MQ=255)
                                                                                ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              >  2:3135715/2‑101 (MQ=255)
                                                                                ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              >  1:2384295/2‑101 (MQ=255)
                                                                                ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              >  1:204009/2‑101 (MQ=255)
                                                                                  ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCTGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            <  2:4031789/101‑1 (MQ=255)
                                                                                  ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            >  2:2656856/1‑101 (MQ=255)
                                                                                   gCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATTACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCCGGGCATTTAACAGTcc           >  2:1118576/1‑101 (MQ=255)
                                                                                   gCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTcc           <  1:1917657/101‑1 (MQ=255)
                                                                                    cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          >  2:3463538/1‑101 (MQ=255)
                                                                                    cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          >  1:572991/1‑101 (MQ=255)
                                                                                    cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          <  1:3710848/101‑1 (MQ=255)
                                                                                      gcgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGAt        <  1:821620/101‑1 (MQ=255)
                                                                                      gcgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCCGGGCATTGAACAGTCCgct        >  1:2551877/1‑99 (MQ=255)
                                                                                       cgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATg       <  1:2159213/101‑1 (MQ=255)
                                                                                       cgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCCACCGGGCAGACGGGATAAAAATCCTCAACCTGGGAATTGAACAGGGCGATg       >  2:543579/1‑101 (MQ=255)
                                                                                        gcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGc      <  1:1356282/101‑1 (MQ=255)
                                                                                          ccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAg    <  2:383716/101‑1 (MQ=255)
                                                                                          ccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAg    <  1:325717/101‑1 (MQ=255)
                                                                                           cccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGc   >  2:143801/1‑101 (MQ=255)
                                                                                            ccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGcc  >  2:1201893/1‑101 (MQ=255)
                                                                                            ccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGcc  >  2:4255872/1‑101 (MQ=255)
                                                                                            ccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGcc  <  2:694536/101‑1 (MQ=255)
                                                                                            |                                                                                                    
GGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGG.CGACCCGCC..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721443‑1721631

Base quality scores:  ATCG  < 3 ≤  ATCG  < 22 ≤  ATCG  < 31 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG