New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 1396470161 (1.030)63 (0.400) 2/132 30.7 0.29 coding (352/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 1397836 = 150 (0.630)intergenic (+140/+1758) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CACCACGGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG..............................................................................  >  NC_014034/1396428‑1396470
.............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCACCTCAG  >  NC_014034/1397836‑1397879
                                           ||||||||||||||||||||||||||||||||||                                            
ggtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGG                      <  2:3943959/91‑1 (MQ=12)
ggtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGG                      >  1:1780407/11‑101 (MQ=12)
ggtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGG                      >  2:2164731/11‑101 (MQ=12)
 gtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGA                     <  1:477244/92‑1 (MQ=12)
 gtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGA                     <  2:3607657/92‑1 (MQ=12)
 gtcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGA                     <  2:3143444/92‑1 (MQ=12)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    >  1:3692723/9‑101 (MQ=17)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  2:1419031/93‑1 (MQ=17)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  1:4507913/93‑1 (MQ=17)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    >  2:2494299/9‑101 (MQ=17)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  2:258215/93‑1 (MQ=17)
  tcaacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                    >  1:4524058/9‑101 (MQ=17)
   caacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGGTC                   >  1:4261340/8‑101 (MQ=12)
   caacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                   <  2:233688/94‑1 (MQ=17)
   caacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                   <  1:3158007/94‑1 (MQ=17)
   caacactGTCGCACCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                   >  1:2528256/8‑101 (MQ=12)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  >  1:1823222/7‑101 (MQ=17)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  >  1:3026687/7‑101 (MQ=17)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  <  1:154476/95‑1 (MQ=17)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  <  1:4392637/95‑1 (MQ=17)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  >  2:1455556/7‑101 (MQ=17)
    aacactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  <  1:4187166/95‑1 (MQ=17)
    aacaCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                  <  2:1727026/97‑1 (MQ=1)
     accctGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 <  1:1937866/96‑1 (MQ=14)
     acactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 >  1:782169/6‑101 (MQ=14)
     acactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 >  1:3940869/6‑101 (MQ=14)
     acactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 >  2:178334/6‑101 (MQ=14)
     acactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 >  1:165982/6‑101 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                >  1:4216720/5‑101 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                >  1:4390574/5‑101 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                >  2:1610708/5‑101 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                <  2:2197567/97‑1 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                <  1:218179/97‑1 (MQ=14)
      cactGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                >  1:1808681/5‑101 (MQ=14)
       cctGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA               <  1:1424812/98‑1 (MQ=14)
       actGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA               >  1:2267642/4‑101 (MQ=14)
        ccgaggtttCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC              >  2:1332394/10‑101 (MQ=0)
         tGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt             <  2:2221824/100‑2 (MQ=1)
         tGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt             >  2:1752721/2‑100 (MQ=1)
         tGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt             >  1:3095857/2‑100 (MQ=1)
          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtc            >  2:2680248/1‑99 (MQ=1)
          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtc            >  1:3860529/1‑99 (MQ=1)
          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtc            <  1:2917010/101‑3 (MQ=1)
          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCGTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtc            >  2:764895/1‑99 (MQ=1)
           TCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCG           <  2:4612903/101‑1 (MQ=1)
            CGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGG          >  2:3006223/1‑101 (MQ=1)
            CGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGG          >  1:572720/1‑101 (MQ=1)
             GCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGGTCCAAACCCGGC         >  1:869624/1‑101 (MQ=0)
             GCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGC         >  1:3204648/1‑101 (MQ=1)
             GCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGC         >  1:974881/1‑101 (MQ=1)
               TCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCct       >  1:2581699/1‑99 (MQ=1)
               TCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCct       >  1:2141991/1‑99 (MQ=1)
               TCCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCct       >  2:340878/1‑99 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctc      <  2:981971/101‑4 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctc      <  1:4471781/101‑4 (MQ=1)
                CCCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctc      >  1:2991329/1‑98 (MQ=1)
                 CCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcg     <  1:2700506/101‑5 (MQ=1)
                 CCCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcg     >  1:496224/1‑97 (MQ=1)
                  CCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcga    >  1:2507218/1‑96 (MQ=1)
                  CCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcga    <  2:4425292/101‑6 (MQ=1)
                  CCCCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcga    <  2:206285/101‑6 (MQ=1)
                    CCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcgatc  <  1:3868899/101‑8 (MQ=1)
                    CCGCGGGGGCGTGGATCGAAACGCTGGCGCGCGCCGCGCCGGATCTTTGTCTGCGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCGGCctcgatc  <  2:850229/101‑8 (MQ=1)
                                           ||||||||||||||||||||||||||||||||||                                            
CACCACGGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG..............................................................................  >  NC_014034/1396428‑1396470
.............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCACCTCAG  >  NC_014034/1397836‑1397879

Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG