New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1396204	131 (0.810)	48 (0.300)	11/136	22.5	0.42	coding (86/1578 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.

GCCACGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCG........................................................................  >  NC_014034/1396157‑1396204 ................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCG  >  NC_014034/1434680‑1434719                                                 ||||||||||||||||||||||||||||||||                                         ccggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCG                     >  1:1087329/9‑101 (MQ=0) ccggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCG                     >  1:3759662/9‑101 (MQ=0)  cggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGg                    >  2:4355194/8‑100 (MQ=0)   ggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGcg                   >  2:1789652/7‑99 (MQ=0)   ggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTG                   >  1:3895311/7‑101 (MQ=0)   ggcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTG                   >  1:2185480/7‑101 (MQ=0)    gcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGG                  <  1:1600546/96‑1 (MQ=0)    gcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGG                  >  2:2897103/6‑101 (MQ=0)    gcccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGG                  <  2:3650078/96‑1 (MQ=0)      ccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGAT                <  1:2928945/98‑1 (MQ=0)      ccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGAT                >  1:1510315/4‑101 (MQ=0)      ccgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGAGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGAT                >  2:4160386/4‑101 (MQ=0)       cgGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATC               >  1:3799599/3‑101 (MQ=1)        gGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCG              >  2:1910619/2‑101 (MQ=1)        gGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCG              <  1:2679106/100‑1 (MQ=1)        gGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCG              >  2:4387900/2‑101 (MQ=1)        gGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCG              >  1:4523734/2‑101 (MQ=1)        gGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCG              <  1:1772665/100‑1 (MQ=1)         GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA             <  1:615492/101‑1 (MQ=1)         GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA             <  2:2152904/101‑1 (MQ=1)          CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA            >  2:1687099/1‑101 (MQ=1)          CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA            <  1:1735309/101‑1 (MQ=1)           GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA           <  2:1079909/101‑1 (MQ=1)           GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA           >  1:168826/1‑101 (MQ=1)           GTCCCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA           <  1:632022/101‑1 (MQ=0)            TCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC          >  1:370675/1‑101 (MQ=1)            TCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC          <  1:2522760/101‑1 (MQ=1)            TCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGGGGATCGAAAC          >  1:4118869/1‑101 (MQ=0)              GCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACac        <  1:1373809/101‑3 (MQ=1)              GCTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACac        <  2:4230477/101‑3 (MQ=1)               CTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacc       >  2:3573498/1‑98 (MQ=1)               CTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacc       <  1:1128933/101‑4 (MQ=1)                cCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaccc      <  1:2147643/100‑5 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaccc      >  2:989227/1‑97 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaccc      <  1:4651127/101‑5 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaccc      >  1:3501136/1‑97 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCC      >  1:2878788/1‑101 (MQ=0)                 CCCCCCGCGGGGGCGTGTATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacccc     >  1:1894521/1‑96 (MQ=0)                 CCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacccc     <  2:4080426/101‑6 (MQ=1)                 CCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacccc     <  1:2897319/101‑6 (MQ=1)                 CCCCCCGCGGGGGCGTGCATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACacccc     <  2:1833405/101‑6 (MQ=0)                  CCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCG    <  2:1947760/101‑1 (MQ=0)                  CCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCG    >  1:840427/1‑101 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGa   >  1:4110960/1‑100 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGa   >  1:1966718/1‑100 (MQ=0)                    CCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGaa  >  2:1372603/1‑99 (MQ=0)                    CCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGaa  <  1:4434503/101‑3 (MQ=0)                    CCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCTTCTGGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGaa  <  2:443600/101‑3 (MQ=0)                                                 ||||||||||||||||||||||||||||||||                                         GCCACGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCGGCG........................................................................  >  NC_014034/1396157‑1396204 ................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCG  >  NC_014034/1434680‑1434719 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 38 ≤  ATCG