New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 = 1396198125 (0.810)56 (0.360) 10/130 22.4 0.30 coding (80/1578 nt) RCAP_rcc01307 hypothetical protein
?NC_014034 1397903 = 139 (0.590)intergenic (+207/+1691) RCAP_rcc01307/RCAP_rcc01309 hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CGCGCCGCCACGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.............................................................................  >  NC_014034/1396151‑1396198
...................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCTATGGGAG  >  NC_014034/1397903‑1397944
                                                |||||||||||||||||||||||||||||||||||                                          
cttctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGG                          >  1:203179/11‑101 (MQ=0)
cttctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGG                          >  2:181612/11‑101 (MQ=0)
 ttctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGG                         <  2:3163444/92‑1 (MQ=0)
  tctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGC                        <  2:4665273/93‑1 (MQ=0)
  tctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGC                        <  1:1185588/93‑1 (MQ=0)
  tctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGC                        <  1:1872542/93‑1 (MQ=0)
  tctggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGCATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGC                        <  1:3937364/93‑1 (MQ=0)
    tggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGg                      >  2:2247085/7‑100 (MQ=0)
    tggtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGT                      <  2:874002/95‑1 (MQ=0)
      gtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGG                    <  2:370638/97‑1 (MQ=1)
      gtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGGGG                    >  2:1878486/5‑101 (MQ=0)
      gtgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCCTGG                    <  2:3952715/97‑1 (MQ=0)
       tgcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGA                   >  1:901269/4‑101 (MQ=1)
        gcCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGgagcgac                  <  2:958090/99‑8 (MQ=0)
         cCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:362189/100‑1 (MQ=1)
         cCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:2866016/100‑1 (MQ=1)
          cgtTGCGTCGCTCCCCCCGCGGGGGCCTGGATCGAAACACCCCGAACCTGTCGACGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                <  2:774801/98‑1 (MQ=0)
          CGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGGGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGCCGTGGATCG                >  2:4619420/1‑101 (MQ=0)
          CGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                <  1:1588754/101‑1 (MQ=1)
          CGCTGCGTCGCGCCCCCCGCGGGGGCGTGGATCGAAACTCCCCGAACCTGTCGGCGGCGAACACCGATGCCGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                <  2:3799314/101‑1 (MQ=0)
           GCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA               >  2:573027/1‑101 (MQ=1)
            CTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              >  1:4180787/1‑101 (MQ=1)
            CTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              <  1:4388192/101‑1 (MQ=1)
            CTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              <  1:4626361/101‑1 (MQ=1)
            CTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              <  2:1510206/101‑1 (MQ=1)
             TGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             >  2:3025890/1‑101 (MQ=1)
             TGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             <  2:2065067/101‑1 (MQ=1)
             TGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             >  2:2043302/1‑101 (MQ=1)
              GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAGACCTCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC            <  1:3991238/101‑1 (MQ=0)
              GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC            <  2:1202685/101‑1 (MQ=1)
               CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa           <  2:2771772/101‑2 (MQ=1)
                GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACat          <  1:3312653/101‑3 (MQ=1)
                GTCGCGCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACat          <  1:4581766/101‑3 (MQ=1)
                 TCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatc         <  1:3926598/101‑4 (MQ=1)
                  CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcg        <  2:1231429/101‑5 (MQ=1)
                  CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcg        <  1:1673210/101‑5 (MQ=1)
                  CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcg        <  1:2927772/101‑5 (MQ=1)
                  CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcg        <  2:4330274/101‑5 (MQ=1)
                  CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGGGGATCGACACatcg        >  2:2297310/1‑97 (MQ=0)
                   GCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcga       >  2:2015063/1‑96 (MQ=1)
                    CTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgat      >  2:279151/1‑95 (MQ=1)
                    CTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgat      >  1:202806/1‑95 (MQ=1)
                     cCCCCCCGCGGGGGCGTGGATCGAAACCCCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     <  1:2765150/100‑8 (MQ=0)
                     cCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     <  2:529006/100‑8 (MQ=1)
                     cCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     <  1:1947330/100‑8 (MQ=1)
                     TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     >  1:410738/1‑94 (MQ=1)
                     TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     >  2:3078909/1‑94 (MQ=1)
                     TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatg     >  2:1088950/1‑94 (MQ=1)
                     TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatagatg     >  2:1847543/1‑94 (MQ=1)
                      CCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatga    >  1:4088146/1‑93 (MQ=1)
                       CCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgat   <  1:989310/101‑10 (MQ=1)
                        CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgatc  <  1:2553121/101‑11 (MQ=0)
                        CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgatc  >  1:1722554/1‑91 (MQ=0)
                        CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgatc  >  1:2610532/1‑91 (MQ=0)
                        CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgatc  <  2:2188897/101‑11 (MQ=0)
                        CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACatcgatgatc  <  1:2628110/101‑11 (MQ=0)
                                                |||||||||||||||||||||||||||||||||||                                          
CGCGCCGCCACGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.............................................................................  >  NC_014034/1396151‑1396198
...................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCTATGGGAG  >  NC_014034/1397903‑1397944

Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 31 ≤  ATCG  < 39 ≤  ATCG