New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1396737	153 (0.990)	50 (0.320)	3/130	29.1	0.27	coding (619/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	1434813 =	117 (0.490)					intergenic (‑592/‑366)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

ATCCGTCATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC................................................................................  >  NC_014034/1396696‑1396737 .............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCG  >  NC_014034/1434813‑1434857                                           |||||||||||||||||||||||||||||||||||                                              gtgccgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGG                       <  2:370638/92‑1 (MQ=1)  tgccgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGA                      >  1:901269/9‑101 (MQ=1)    ccgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATC                    <  1:362189/95‑1 (MQ=1)    ccgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATC                    <  1:2866016/95‑1 (MQ=1)     cgttgCGTCGCTCCCCCCGCGGGGGCCTGGATCGAAACACCCCGAACCTGTCGACGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   <  2:774801/96‑1 (MQ=0)     cgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGGGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGCCGTGGATCG                   >  2:4619420/6‑101 (MQ=0)     cgctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                   <  1:1588754/96‑1 (MQ=1)      gctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                  >  2:573027/5‑101 (MQ=1)       ctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 <  2:1510206/98‑1 (MQ=1)       ctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 <  1:4626361/98‑1 (MQ=1)       ctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 <  1:4388192/98‑1 (MQ=1)       ctgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                 >  1:4180787/4‑101 (MQ=1)        tgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                <  2:2065067/99‑1 (MQ=1)        tgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                >  2:2043302/3‑101 (MQ=1)        tgCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                >  2:3025890/3‑101 (MQ=1)         gCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAGACCTCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC               <  1:3991238/100‑1 (MQ=0)         gCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC               <  2:1202685/100‑1 (MQ=1)          CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCCCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACA              <  2:2771772/101‑1 (MQ=1)           GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAT             <  1:3312653/101‑1 (MQ=1)           GTCGCGCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAT             <  1:4581766/101‑1 (MQ=1)            TCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATc            <  1:3926598/101‑2 (MQ=1)             CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATcg           <  1:2927772/101‑3 (MQ=1)             CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATcg           <  2:1231429/101‑3 (MQ=1)             CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATcg           <  2:4330274/101‑3 (MQ=1)             CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATcg           <  1:1673210/101‑3 (MQ=1)             CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGGGGATCGACACATcg           >  2:2297310/1‑99 (MQ=0)              GCTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGA          >  2:2015063/1‑101 (MQ=1)               CTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAt         >  2:279151/1‑100 (MQ=1)               CTCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAt         >  1:202806/1‑100 (MQ=1)                cCCCCCCGCGGGGGCGTGGATCGAAACCCCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        <  1:2765150/100‑3 (MQ=0)                cCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        <  1:1947330/100‑3 (MQ=1)                cCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        <  2:529006/100‑3 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGCACACCGATACCGCGTCGCTCCCACCGCGGGGGCGTGGATCGAAACATCGAtg        >  1:3831201/1‑99 (MQ=0)                TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        >  2:1088950/1‑99 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        >  1:410738/1‑99 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtg        >  2:3078909/1‑99 (MQ=1)                TCCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATAGAtg        >  2:1847543/1‑99 (MQ=1)                 CCCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtga       >  1:4088146/1‑98 (MQ=1)                  CCCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgat      <  1:989310/101‑5 (MQ=1)                   CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatc     <  2:2188897/101‑6 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatc     >  1:1722554/1‑96 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatc     <  1:2553121/101‑6 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatc     <  1:2628110/101‑6 (MQ=0)                   CCCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatc     >  1:2610532/1‑96 (MQ=0)                    CCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatca    <  2:4324849/101‑7 (MQ=0)                    CCCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatca    <  1:3424577/101‑7 (MQ=0)                     CCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatcaa   <  1:558822/101‑8 (MQ=0)                     CCGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatcaa   <  1:3283737/101‑8 (MQ=0)                      CGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatcaaa  <  1:4333768/101‑9 (MQ=0)                      CGCGGGGGCGTGGATCGAAACACCCCGAACCTGTCGGCGGCGAACACCGATACCGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATCGAtgatcaaa  >  1:4095430/1‑93 (MQ=0)                                           |||||||||||||||||||||||||||||||||||                                              ATCCGTCATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC................................................................................  >  NC_014034/1396696‑1396737 .............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCG  >  NC_014034/1434813‑1434857 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG