New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1396738	145 (1.040)	40 (0.290)	9/132	19.6	0.22	coding (620/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	1434349 =	146 (0.690)					intergenic (‑128/‑830)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

CGATCCGTCATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACC.............................................................................  >  NC_014034/1396694‑1396738 ...............................................................................GGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGTCTCCGCTC  >  NC_014034/1434349‑1434391                                              ||||||||||||||||||||||||||||||||||                                            tgtcgctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCG                       >  2:3797186/10‑101 (MQ=0) ccgggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCG                       <  2:3615540/92‑1 (MQ=0)   gggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTG                     <  2:2956261/94‑1 (MQ=0)   gggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTG                     >  2:3260950/8‑101 (MQ=0)   gggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTG                     >  2:4157795/8‑101 (MQ=0)   gggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTG                     <  2:842847/94‑1 (MQ=0)    ggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGG                    <  1:1908074/95‑1 (MQ=0)    ggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGG                    >  1:3549763/7‑101 (MQ=0)    ggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGG                    <  1:675236/95‑1 (MQ=0)    ggctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGGGG                    >  1:3226153/7‑101 (MQ=0)     gctcgATCGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGA                   <  2:2341545/96‑1 (MQ=0)      ctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGAT                  <  2:54917/97‑1 (MQ=1)      ctcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGAT                  <  1:1184727/97‑1 (MQ=1)       tcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  2:1766922/98‑1 (MQ=1)       tcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:3930233/98‑1 (MQ=1)       tcgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATC                 <  1:2672350/98‑1 (MQ=0)        cgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                <  2:4150910/99‑1 (MQ=1)        cgATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                >  1:3087753/3‑101 (MQ=1)         gATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA               >  2:2944841/2‑101 (MQ=1)         CATCGTCGCTCCCCCCGCGGGGACGTGGATCGAATCCTATGAGGGCTGGCGGCCCGGTCGTTGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA               <  2:3165394/101‑1 (MQ=0)          ATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA              >  1:1854199/1‑101 (MQ=1)          ATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGGGGGTCGAA              >  1:42687/1‑101 (MQ=0)           TCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA             <  2:1052830/101‑1 (MQ=1)            CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC            >  2:2306886/1‑101 (MQ=1)            CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC            <  1:2016934/101‑1 (MQ=1)             GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa           >  1:2729630/1‑100 (MQ=1)             GTCACTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa           <  1:3797446/101‑2 (MQ=1)              TCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGGGGATCGAAACat          >  1:1181134/1‑99 (MQ=1)               CGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATC         >  2:1806113/1‑101 (MQ=1)               CGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATC         >  2:448201/1‑101 (MQ=1)                gcgCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCa        <  2:3236630/98‑2 (MQ=11)                gccCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCa        <  1:4474/98‑2 (MQ=11)                GCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCa        >  1:632701/1‑100 (MQ=11)                GCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCa        <  1:2476252/101‑2 (MQ=11)                  TCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagc      >  2:1754110/1‑98 (MQ=32)                  TCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagc      >  1:2246081/1‑98 (MQ=32)                   CCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagct     >  2:2389395/1‑97 (MQ=33)                   CCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagct     <  1:162541/101‑5 (MQ=33)                    CCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagctt    >  1:877473/1‑96 (MQ=18)                      CCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCagcttga  <  1:3736459/101‑8 (MQ=18)                                              ||||||||||||||||||||||||||||||||||                                            CGATCCGTCATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACC.............................................................................  >  NC_014034/1396694‑1396738 ...............................................................................GGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGTCTCCGCTC  >  NC_014034/1434349‑1434391 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG