New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 1396902 =152 (0.970)46 (0.290) 6/132 26.2 0.24 coding (784/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 = 1397934 141 (0.590)intergenic (+238/+1660) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

GCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG............................................................................  <  NC_014034/1396949‑1396902
..................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAG  <  NC_014034/1397934‑1397893
                                                ||||||||||||||||||||||||||||||||||                                          
catggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCG                         <  2:909289/96‑1 (MQ=0)
catggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCG                         <  1:1833621/96‑1 (MQ=0)
catggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCG                         <  2:1919169/96‑1 (MQ=0)
 atggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGC                        <  1:1409708/97‑1 (MQ=0)
 atggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGC                        >  2:3351284/5‑101 (MQ=0)
   ggCGCGCACGCAGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGG                      <  2:1050101/99‑1 (MQ=0)
   ggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGG                      <  2:2178612/99‑1 (MQ=0)
   ggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGG                      >  2:1614773/3‑101 (MQ=0)
   ggCGCGCACGCAGTTTCGATCCACGCCCCCACGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGG                      <  2:2460396/99‑1 (MQ=0)
     CGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGG                    <  2:1030456/101‑1 (MQ=0)
     CGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGG                    <  1:463628/101‑1 (MQ=0)
      GCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGG                   >  2:3769477/1‑101 (MQ=0)
       CGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:2478808/101‑1 (MQ=1)
       CGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:651747/101‑1 (MQ=1)
        GCACGCAGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGA                 <  2:1642097/101‑1 (MQ=0)
        GCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCCTTGTTTCGATCCACGCCCCCGCGGGGGGc                 >  2:985805/1‑100 (MQ=0)
        GCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGg                 >  1:2901129/1‑100 (MQ=1)
        GCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGA                 <  2:4549592/101‑1 (MQ=1)
         cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAG                >  1:365563/7‑101 (MQ=1)
         cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAG                <  1:3649725/95‑1 (MQ=1)
         cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAG                >  1:2065742/7‑101 (MQ=1)
          acgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGC               >  1:760688/6‑101 (MQ=1)
          acgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGC               >  2:2766028/6‑101 (MQ=1)
           cgcatttcCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  1:511801/93‑1 (MQ=0)
           cgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCG              >  2:3742984/5‑101 (MQ=1)
           cgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  2:2811199/97‑1 (MQ=1)
           cgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  2:2345066/97‑1 (MQ=1)
            gcaGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             <  1:4430899/98‑1 (MQ=1)
            gcaGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             <  1:871063/98‑1 (MQ=1)
            gcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             >  1:1822421/4‑101 (MQ=1)
              aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACg           >  2:3487898/2‑100 (MQ=1)
              aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg           >  1:1143537/2‑100 (MQ=1)
               GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgt          <  1:4591596/101‑3 (MQ=1)
                TTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtg         <  1:4471838/101‑4 (MQ=1)
                 TTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgc        >  2:2337729/1‑97 (MQ=1)
                 TTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgc        >  2:2955621/1‑97 (MQ=1)
                   CGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACgggcgg      >  1:253318/1‑95 (MQ=0)
                    GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACgtgcgag     >  2:4053094/1‑94 (MQ=0)
                    GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgag     <  1:3028630/101‑8 (MQ=0)
                    GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgag     >  1:3056539/1‑94 (MQ=0)
                    GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgag     <  2:363785/101‑8 (MQ=0)
                    GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgag     >  2:110012/1‑94 (MQ=0)
                     ATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACgtgcgagg    >  1:3482606/1‑93 (MQ=0)
                      TCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgaggg   <  1:1213048/101‑10 (MQ=0)
                       CCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagggc  <  2:2743125/101‑11 (MQ=0)
                       CCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagggc  >  1:89064/1‑91 (MQ=0)
                                                ||||||||||||||||||||||||||||||||||                                          
GCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG............................................................................  <  NC_014034/1396949‑1396902
..................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAG  <  NC_014034/1397934‑1397893

Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG