New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1397599	153 (0.950)	44 (0.270)	10/132	17.5	0.37	coding (1481/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	1434547 =	0 (0.000)					intergenic (‑326/‑632)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

GCCGCGCTGACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACA............................................................................  >  NC_014034/1397556‑1397599 ..............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGA  >  NC_014034/1434547‑1434588                                             ||||||||||||||||||||||||||||||||||                                           ggccctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTG                     <  2:4742153/92‑1 (MQ=0)  gccctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGG                    <  1:2991359/93‑1 (MQ=0)   ccctcggcCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGA                   <  2:1474945/93‑1 (MQ=0)   ccctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGA                   <  1:62857/94‑1 (MQ=0)   ccctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGA                   <  1:1817183/94‑1 (MQ=0)    cctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGAT                  >  1:4396343/7‑101 (MQ=0)    cctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGGGGAT                  >  1:3464217/7‑101 (MQ=0)     ctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:1558154/96‑1 (MQ=1)     ctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  2:1969226/96‑1 (MQ=1)     ctcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:1714703/96‑1 (MQ=1)      tcgccCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCG                <  1:2141665/96‑1 (MQ=1)      tcgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCG                >  2:2841841/5‑101 (MQ=1)       cgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGCTCGA               >  1:2880496/4‑101 (MQ=0)       cgcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGA               <  1:392385/98‑1 (MQ=1)        gcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              <  1:3695411/99‑1 (MQ=1)        gcACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGGGGATCGAA              >  1:4421915/3‑101 (MQ=1)         cACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             <  2:1126459/100‑1 (MQ=1)         cACGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             <  2:3738254/100‑1 (MQ=1)           CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAGCAATGCGGCGCGGGCCTATGGCTGCCGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt           <  1:1650046/101‑2 (MQ=0)           CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt           <  2:3899138/101‑2 (MQ=1)           CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACt           <  2:3384717/101‑2 (MQ=1)           CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCCCGGGGGCGTGGATCGAAAat           >  1:4809832/1‑99 (MQ=1)            GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGGTTGAAAatg          >  2:1754202/1‑98 (MQ=0)            GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtg          >  1:4009300/1‑99 (MQ=1)            GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtg          <  2:392077/101‑3 (MQ=1)            GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtg          >  2:4192343/1‑99 (MQ=1)            GTCGCCCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGCCCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtg          <  2:2700608/101‑3 (MQ=0)            GTCGCCCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtg          <  1:4639615/101‑3 (MQ=1)             gccccCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGCCCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgc         <  2:4448557/96‑4 (MQ=0)             TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgc         >  1:55929/1‑98 (MQ=1)             TCGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgc         <  1:5053765/101‑4 (MQ=1)             TCGCCCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgc         <  1:1522818/101‑4 (MQ=0)              CGCTCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcg        >  1:2610296/1‑97 (MQ=1)               gccCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgt       <  1:4462868/98‑6 (MQ=0)                 cCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgc     <  1:3062797/100‑8 (MQ=0)                 cCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgc     <  2:4506471/100‑8 (MQ=0)                 cCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgc     <  1:1271511/100‑8 (MQ=0)                 TCCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgc     >  1:549801/1‑94 (MQ=0)                  CCCCCCGCGGGGGCTTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgcg    <  2:3510005/101‑9 (MQ=0)                  CCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgcg    <  2:1711472/101‑9 (MQ=0)                  CCCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgcg    <  1:1300738/101‑9 (MQ=0)                   CCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgcgc   >  1:2126314/1‑92 (MQ=0)                   CCCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTGCGCGCgc   >  2:3498382/1‑99 (MQ=0)                    CCCCGCGGGGGCGTGGATCGAAACAATGCGGCGCGGGCCTATGGCTGACGGACCCGCCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACtgcgtgcgcg  <  2:2661674/101‑11 (MQ=0)                                             ||||||||||||||||||||||||||||||||||                                           GCCGCGCTGACGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACA............................................................................  >  NC_014034/1397556‑1397599 ..............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGA  >  NC_014034/1434547‑1434588 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG