New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	510059 =	53 (0.230)	19 (0.080)	2/198	36.0	0.26	intergenic (+46/+141)	RCAP_rcc00475/RCAP_rcc00476	acyl‑CoA dehydrogenase domain‑containing protein/hypothetical protein
	?	NC_014034	1253894 =	53 (0.230)					intergenic (+52/+39)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

ATCGAAAGCGGGTCCGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAGGGGCCCTGCC  >  NC_014034/509963‑510159                                                                                                         |                                                                                                       aTCGAAAGCGGGTCCGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.ggggg                                                                                                    >  1:720214/1‑101 (MQ=255)  tCGAAGGCGGGTCGGGGGGGGTGAGGGGGCGCTCGGCCGATCAGTTCTGAGCGGGAGGGGTTTTCG.CCCG.GGGCTTGCGCCG.GGG.G.CGACCCGC..C.GGGGGc                                                                                                   <  2:620473/101‑1 (MQ=25)    gAAAGCGGGTCCGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGGCCCGC..C.gggggggc                                                                                                 >  1:4099522/1‑98 (MQ=255)     aaaGCGGGTCCGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGCGcc                                                                                                >  2:2074690/1‑101 (MQ=255)          gggTCGGGGGGGGTGAGGGGGCTCTCGGCCGATCAGTTCTGGGCGGCGGGGGTTTCCC.CCCC.GGGTTTGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.c.ccc                                                                                         <  1:2853994/101‑1 (MQ=25)             gcggggggggTGATGGGCCCCGCGGCCGATCAGTTCTGGGGGGCGGGGGTTTTCG.CCCG.GGGCTTGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCgg                                                                                      <  2:4321120/96‑1 (MQ=21)              cggggggggTTTTGGGGCTGGGGGCGGTTTAGTTGGGAGCGGGGTGGGTTTCCT.CCCG.GGGTTTGCGCCC.GGG.G.GAACCCGC..C.GGGGGCTCCG.C.CCCCGGa                                                                                     <  1:468435/97‑1 (MQ=9)              cggggggggTGGGGGGGCTCGCGCCCGTCGAGTTCGGAGGGGCGGGGGTTCCCG.CCCG.GGGCTTGCCCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGa                                                                                     <  2:21674/97‑1 (MQ=12)              cggggggggTGGGGGGGCTCCGGGCCGATCAGTTCTGAGGGGGGGGGGTTTCCG.CCCG.GGGCTGGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGa                                                                                     <  2:46190/97‑1 (MQ=16)               cGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCTGCAGGGGATTTCT.CCCA.GGGCTTGCGCCC.GGG.G.CGACCCGC..CTGGGCGCTCAC.C.CCCCgcc                                                                                     >  2:2957849/1‑99 (MQ=37)               cGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGCTccagatcggaag                                                                                      >  2:3502815/1‑91 (MQ=255)                gAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGTCCC.c.cccccgccc                                                                                   >  1:2044393/1‑96 (MQ=255)                gAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGCCC.c.cccccgccc                                                                                   >  1:1893129/1‑96 (MQ=37)                 ggggggTGGGGGGGCTCTCGGCCGATCGGTTGTGAGGGGCGGGGGTTTCCC.CCCC.GGCCTTGCGCCG.GGG.C.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGAccc                                                                                  <  1:1802373/100‑1 (MQ=16)                 aGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGCCGC.GGGGGCGCGG.C.CCCCgccc                                                                                    >  2:1528789/1‑98 (MQ=25)                  gggggTGAGGGGGCTCCCGGCCGATCGTTTCTGCGCGG.GGGGGTTTTCC.CCCCGGGGCTTGCGCCC.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGAcccc                                                                                 <  2:2048375/101‑1 (MQ=16)                   ggggTGGGGGGGCCCCCGGCCGTTCATTTCGGGGGGGCGGGGGTTTCCG.CCCG.GGGTTTGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGAccccc                                                                                <  2:2583375/101‑1 (MQ=12)                       tGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGCCG.CGCCCCCGCcccccccc                                                                             >  2:2600634/1‑98 (MQ=25)                       tGATGGGCCTCTCGGCCGATCATTTCTGGGCGGCGGGGGTTTCCG.CCCC.GGGCTTGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGAc                                                                            <  2:457846/101‑1 (MQ=25)                       gtaTGGGGCTCTCGGCCGATCATTTCTGAGCGGCGGGGGTTTCCG.CCCC.GGGCTTGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGAc                                                                            <  2:1952247/99‑1 (MQ=25)                           ggggCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.CGGGGGGCCC.C.CCCCCGGCCCCCCCACTTcc                                                                        >  1:2097671/1‑100 (MQ=25)                                cctcGGCGGATCAGTTGGGGGGGGGGGGGGTTTCCG.CCCC.GGGTTCGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGc                                                                   <  1:3297343/100‑1 (MQ=16)                                  ccgcccGCTCAGTTCTGGGGGGGGGGGGTTTCCG.CCCC.GGGCTGGCCCCG.GGG.C.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGt                                                                 <  2:811632/97‑1 (MQ=19)                                   cgcccGATCAGTTCTGGGGGGGGGGGTTTTCCG.CCCC.GGGCGGGCGCCC.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTa                                                                <  2:553510/98‑1 (MQ=21)                                     gCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGCCC.C.CCCCCGGCCCCCCCACTTCTGATGCggctt                                                              >  2:1963958/1‑97 (MQ=21)                                       ccgtCAGTTCTGTGGGGGGGGGAATTGCG.GCAG.GGGCTTGCGCCC.GGG.C.CCACCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTg                                                            <  2:1355188/98‑1 (MQ=21)                                        gATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGCCG.C.CCCCCGGCCCCCCCCCTTCCGATGCGTAttttg                                                           >  2:1880205/1‑99 (MQ=21)                                           cggTTCGGAGGGGCGGGGGTTTTCG.CCCC.GGGCTTGCCCCG.GGG.C.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGcc                                                        <  2:432313/99‑1 (MQ=25)                                            ggttcgggggggCGGGGGCTTCCG.CCCG.GGGCTGGCGCCC.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCa                                                       <  1:2652519/91‑1 (MQ=25)                                              tgcgggggggCAGGGTATTCCC.CCCG.GGGCTTCCGCCC.GGG.C.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAg                                                     <  2:2097534/93‑1 (MQ=25)                                                    gcggggggggTTTCCC.CCCC.GGGCTGGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAg                                               <  1:3353680/95‑1 (MQ=25)                                                       gggggggGTTTCGCCCCC.GGGCGTGCCCCCGGGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGc                                              <  1:1513174/98‑1 (MQ=25)                                                       gCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGCCGCC.CCCCGGGCCCCCTCCCTT.ACATGCGGTTTTTAGTCAAAaaaaaagcc                                            >  2:2968572/1‑97 (MQ=9)                                                        gcggggGTTTCC.CCCC.CGGCCTGCCCCC.GGG.GCCCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCg                                            <  1:1964087/99‑1 (MQ=25)                                                             gATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGGGGCGCC.CCCCGGCCCCCCCCCCTTC.CATGCGTATTTTTGCCAAGaaaaaaaagacaagc                                      >  2:524273/1‑91 (MQ=9)                                                                  ccccccc.GGGCTGGCGCCC.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCtt                                  <  1:3392300/98‑1 (MQ=255)                                                                   g.CCCC.GGGCTTGCGCCG.GGG.C.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCtttt                                <  1:2600805/101‑1 (MQ=255)                                                                    ccccc.GGGGTTGCGCCG.GGG.G.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCtttt                                <  2:3955039/100‑1 (MQ=38)                                                                    ccccc.GGGCGGGCGCCG.GGG.G.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCtttt                                <  1:296391/100‑1 (MQ=38)                                                                     cccc.GGGGCTGCCCCC.GGGCG.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCtttt                                <  2:3659703/101‑1 (MQ=37)                                                                       gc.GGGTTGGCGCCC.GGC.C.GGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCTCTTTTGAg                             <  1:556224/100‑1 (MQ=37)                                                                        cggggCTTGCGCGG.GGG.C.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAg                             <  1:469075/99‑1 (MQ=38)                                                                         ggggcgcgccccc.GGG.G.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAgg                            <  1:372024/91‑1 (MQ=38)                                                                                   cccgggg.g.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAAt                   <  1:2503128/97‑1 (MQ=255)                                                                                    ccgggg.g.CCCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAAtt                  <  1:604989/98‑1 (MQ=255)                                                                                      ccggtgccgccccGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAAtt                  <  2:4316061/91‑1 (MQ=255)                                                                                        gg.g.CGCCCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGaaa              <  1:1880329/101‑1 (MQ=255)                                                                                           gcccccccGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGaaaa             <  1:436488/96‑1 (MQ=255)                                                                                            gccccccGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAg            <  1:294252/97‑1 (MQ=255)                                                                                             ccccccGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAgg           <  2:1523721/98‑1 (MQ=255)                                                                                               ccccGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAgggg         <  2:4099262/100‑1 (MQ=255)                                                                                                   gc..c.gGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAGGGGCCCt     <  2:1894022/101‑1 (MQ=255)                                                                                                    c..c.gGGGGCTCCG.C.CCCCGGACCCCCTGACTTCATATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAGGGGCCCTg    <  1:3836354/101‑1 (MQ=255)                                                                                                         gggggCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAGGGGCCCTGcc  <  1:2342940/101‑1 (MQ=255)                                                                                                         |                                                                                                       ATCGAAAGCGGGTCCGAGGGGGTGATGGGGCTCTCGGCCGATCAGTTCTGAGCGGCAGGGGATTTCG.CCCC.GGGCTTGCGCCC.GGG.G.CGACCCGC..C.GGGGGCTCCG.C.CCCCGGACCCCCTGACTTCAGATGCGTATTTGAGCCAAGAAAAAGCCGACAGGCGCTTTTGAGGTTCGGAAATTGAAAAGGGGCCCTGCC  >  NC_014034/509963‑510159 Base quality scores:  ATCG  < 3 ≤  ATCG  < 21 ≤  ATCG  < 31 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG