New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 1397533242 (1.470)53 (0.320) 5/134 21.4 0.30 coding (1415/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 1434680 = NA (NA)intergenic (‑459/‑499) RCAP_rcc01334/RCAP_rcc01335 hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

CGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG  >  NC_014034/1434581‑1434778
                                                                                                   |                                                                                                    
cgcgCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGt                                                                                                     <  1:1693989/101‑1 (MQ=255)
cgcgCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGt                                                                                                     <  1:3720461/101‑1 (MQ=255)
cgcgCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGt                                                                                                     <  1:2461071/101‑1 (MQ=255)
   gcTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCGGTCGc                                                                                                  >  2:2997099/1‑101 (MQ=255)
   gcTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGc                                                                                                  <  1:4803967/101‑1 (MQ=255)
   gcTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGc                                                                                                  >  1:1199404/1‑101 (MQ=255)
    cTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCCTGGCGCCGAGGGACAGGCTTTGCAGTCGCt                                                                                                 >  1:3722136/1‑101 (MQ=255)
    cTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCTCCGAGGGACAGGCTTTGCAGTCGCt                                                                                                 >  1:4605910/1‑101 (MQ=255)
    cTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCt                                                                                                 <  1:4867029/101‑1 (MQ=255)
     tGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTc                                                                                                >  2:4982596/1‑101 (MQ=255)
     tGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTc                                                                                                >  2:2997885/1‑101 (MQ=255)
     tGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTc                                                                                                >  1:2935090/1‑101 (MQ=255)
     tGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTc                                                                                                <  2:3861127/101‑1 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               <  2:2052379/101‑1 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               <  1:2476360/101‑1 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               <  1:70592/101‑1 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               <  2:3675603/101‑1 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               >  2:4290942/1‑101 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               >  1:3367896/1‑101 (MQ=255)
      gAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcc                                                                                               >  1:3644535/1‑101 (MQ=255)
       aaGGAGTGTGCTCCCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTccc                                                                                              <  2:48499/101‑1 (MQ=255)
       aaGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGTGCCGAGGGACAGGCTTTGCAGTCGCTccc                                                                                              <  1:583722/101‑1 (MQ=255)
       aaGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTccc                                                                                              <  1:1770821/101‑1 (MQ=255)
       aaGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTccc                                                                                              <  2:1380973/101‑1 (MQ=255)
       aaGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTccc                                                                                              >  2:4289600/1‑101 (MQ=255)
        aggaggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcccc                                                                                             >  1:3637086/1‑101 (MQ=255)
         ggaggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTccccc                                                                                            <  1:4415760/101‑1 (MQ=255)
          gaggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcccccc                                                                                           <  1:4981190/101‑1 (MQ=255)
          gaggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcccccc                                                                                           <  1:2211653/101‑1 (MQ=255)
          gaggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTcccccc                                                                                           <  1:840975/101‑1 (MQ=255)
           aggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCcg                                                                                          <  1:1095170/101‑1 (MQ=255)
           aggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCcg                                                                                          >  2:2958464/1‑101 (MQ=255)
           aggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCcg                                                                                          <  2:1618019/101‑1 (MQ=255)
           aggGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCcg                                                                                          <  1:1907831/101‑1 (MQ=255)
             ggTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCcgcg                                                                                        >  2:3799005/1‑101 (MQ=255)
                gATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCgggg                                                                                     <  2:4758957/101‑1 (MQ=255)
                 aTCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCggggg                                                                                    >  1:2841296/1‑101 (MQ=255)
                   ctcGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCg                                                                                  >  2:4074715/1‑101 (MQ=40)
                   ctcGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCg                                                                                  >  2:2771658/1‑101 (MQ=40)
                    tcGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCgg                                                                                 >  2:4797526/1‑100 (MQ=39)
                     cGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTg                                                                                <  1:749733/101‑1 (MQ=38)
                     cGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTg                                                                                >  1:3301751/1‑101 (MQ=38)
                     cGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTg                                                                                <  1:3319967/101‑1 (MQ=38)
                      ggTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTgg                                                                               >  2:3839490/1‑101 (MQ=37)
                      ggTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTgg                                                                               <  2:4099077/101‑1 (MQ=37)
                      ggTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTgg                                                                               >  1:543484/1‑101 (MQ=37)
                      ggTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTgg                                                                               <  1:5011130/101‑1 (MQ=37)
                       gTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGa                                                                              <  1:599601/101‑1 (MQ=35)
                       gTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGa                                                                              <  1:3815684/101‑1 (MQ=35)
                        tGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGAt                                                                             >  2:3481003/1‑101 (MQ=34)
                        tGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGAt                                                                             >  2:4097223/1‑101 (MQ=34)
                        tGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGAt                                                                             <  1:2649894/101‑1 (MQ=34)
                         ggCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATc                                                                            <  2:3418397/101‑1 (MQ=33)
                         ggCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATc                                                                            <  2:4381716/101‑1 (MQ=33)
                          gcgcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCg                                                                           <  1:699237/101‑1 (MQ=32)
                          gcgcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCg                                                                           <  1:507898/101‑1 (MQ=32)
                          gcgcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCg                                                                           >  1:329811/1‑101 (MQ=32)
                            gcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGaa                                                                         <  1:2376137/101‑1 (MQ=11)
                            gcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGaa                                                                         >  1:3215105/1‑101 (MQ=11)
                            gcCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGGGGATCGaa                                                                         >  1:3452086/1‑101 (MQ=11)
                            gcCTTGTCGCGCCCCCCGCGGGGGCGTGGCGCGAAACCCGGATTGCATGGCGCCGAGGGACCGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGaa                                                                         <  2:1470479/101‑1 (MQ=11)
                                                                                                   gTCGCCCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAaca  <  1:1015311/101‑2 (MQ=2)
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CGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG  >  NC_014034/1434581‑1434778

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG