New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 1396335158 (0.960)46 (0.280) 3/134 23.3 0.23 coding (217/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 1397836 = 154 (0.630)intergenic (+140/+1758) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

ACTTCTGTTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAA..............................................................................  >  NC_014034/1396292‑1396335
.............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCACCTCAGC  >  NC_014034/1397836‑1397880
                                            |||||||||||||||||||||||||||||||||                                             
agcggctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGG                       <  1:82140/91‑1 (MQ=0)
 gcggctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGA                      <  1:477855/92‑1 (MQ=0)
 gcggctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGA                      <  2:1302225/92‑1 (MQ=0)
  cggctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGAT                     <  1:54187/93‑1 (MQ=1)
  cggctgcgGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGAT                     <  2:206686/93‑1 (MQ=0)
   ggctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATC                    >  2:3739807/8‑101 (MQ=1)
    gctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   >  1:1007183/7‑101 (MQ=1)
    gctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   <  1:3621198/95‑1 (MQ=1)
    gctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   <  2:1961055/95‑1 (MQ=1)
    gcggcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   <  2:3585850/95‑1 (MQ=1)
     ctgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                  <  2:2718213/96‑1 (MQ=1)
     ctgcgGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                  <  1:1754332/96‑1 (MQ=1)
      tgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 <  2:2101507/97‑1 (MQ=1)
      tgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 >  2:1840076/5‑101 (MQ=1)
      tgcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 <  2:4062006/97‑1 (MQ=1)
       gggGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                <  1:642809/98‑1 (MQ=1)
       gcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                <  1:3846625/98‑1 (MQ=1)
       gcgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                >  1:1266709/4‑101 (MQ=1)
        cgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC               <  2:3173527/99‑1 (MQ=1)
         gGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACC              >  1:4112736/2‑101 (MQ=1)
         gGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACC              <  1:3701546/100‑1 (MQ=1)
          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCC             <  2:3134417/101‑1 (MQ=1)
           TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCc            <  1:4543318/101‑2 (MQ=1)
           TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCc            <  1:4517310/101‑2 (MQ=1)
           TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCc            <  1:2411224/101‑2 (MQ=1)
           TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCc            >  1:2185868/1‑100 (MQ=1)
             GCTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGC          <  1:3928218/101‑1 (MQ=1)
              CTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCcccg         >  2:908102/1‑97 (MQ=1)
              CTCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCg         >  1:640531/1‑100 (MQ=1)
               TCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCgg        >  1:2280190/1‑99 (MQ=1)
               TCCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCgg        <  2:4644622/101‑3 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggc       >  2:3670788/1‑98 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggc       >  2:4398618/1‑98 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggc       <  2:974032/101‑4 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggc       >  1:780972/1‑98 (MQ=1)
                 CCCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcg      >  2:3079507/1‑97 (MQ=0)
                  CCCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgt     >  1:2193081/1‑96 (MQ=0)
                   CCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtc    <  1:432345/101‑7 (MQ=0)
                   CCCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtc    <  2:3830578/101‑7 (MQ=0)
                    CCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtcc   <  2:2666269/101‑8 (MQ=0)
                    CCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtcc   <  2:2375870/101‑8 (MQ=0)
                    CCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtcc   <  1:4175887/101‑8 (MQ=0)
                    CCGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtcc   >  1:1111164/1‑94 (MQ=0)
                     CGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtccc  <  2:3933493/101‑9 (MQ=0)
                     CGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtccc  <  1:4228479/101‑9 (MQ=0)
                     CGCGGGGGCGTGGATCGAAACAAAAAGCCGCCGACAAACGCGGCAACCGGCCCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCggcgtccc  <  1:1554231/101‑9 (MQ=0)
                                            |||||||||||||||||||||||||||||||||                                             
ACTTCTGTTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAA..............................................................................  >  NC_014034/1396292‑1396335
.............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCACCTCAGC  >  NC_014034/1397836‑1397880

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG