New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253890	28 (0.130)	33 (0.150)	4/192	33.1	0.52	intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 1721531	34 (0.150)					intergenic (‑426/+20)	RCAP_rcc01588/RCAP_rcc01589	GSCFA family protein/ErfK/YbiS/YcfS/YnhG family protein
Rejected: Position hash score below cutoff.

GCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGG.CCGGTCGCCTTGGGGATTTCGCCTC.GG.CTGCGCCGAGGCGA.CCCGCC..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721435‑1721631                                                                                                       |                                                                                                     gcgcTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGG.CCGGTCGCCTTGGGGATTTCGCCTC.GG.CTGCGCCGAGGCGA.CCCGCCGGGGGCTGCGCCCCCg                                                                                                    >  2:4365923/1‑101 (MQ=255)              ccctcccGCAGCGCTTTATTTTTGG.CCGGTCGCCTTGGGGATTTCGCCTC.GG.CTGCGCCGAGGCGA.CCCGCC..CCGCGGGGCGCCCGCGccgcccccccccc                                                                                     >  1:1610848/1‑96 (MQ=25)                 ccccGCGTCGTTTTGTTTGGGG.CCGGGCGCTGGGGGGTTTCCCCCGC.GG.CGGCCCGGGGGCCC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGAt                                                                                    <  2:2619071/100‑1 (MQ=2)                    cgcggctttttTTTTTGGG.CCGGCCG.CTTGGGGTTTTCCCCCCGGG.CGGCGCCGAGCCGC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGAtctc                                                                                 <  2:645687/93‑1 (MQ=9)                            tttTTTTTTGG.GCGGGCCGCGTGGGGTTTTCCCCCC.GG.GCCCCCCGGGGCCACCCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCAc                                                                          <  1:1060187/101‑1 (MQ=255)                                tttttGGCCCGGTCGCCTGGGGGTTCCCCCCCC.GG.CGGCGCGGAGCCGC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTg                                                                      <  1:2502725/101‑1 (MQ=255)                                ttttgtg.CCCGTCCCCTTTGGGGTTTCCCCCC.GGCCTCCCCCGAGCCCC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTg                                                                      <  2:3745397/95‑1 (MQ=255)                                           gtcgctggggggTTTCCGCCGC.GG.GGGCGCCGGGCCCC.CCCGCCGGGGGCTGCGCCCCCGGCCCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGcc                                                           <  1:2764243/93‑1 (MQ=255)                                               ctggggggCTTCCCCCCC.GG.CGGCCCCGCGGCCC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGAcc                                                       <  1:274110/97‑1 (MQ=255)                                                   ggggATTTCGCCTC.GG.CTGCGCCGAGGCGA.CCCGCCGGGGGGTGCGCCCCCGGAGCCCCCCCCAAGAAATCAGAACACCTTTACCTCCGGGGCGACCcggg                                                   >  2:2106738/1‑100 (MQ=9)                                                               gc.GG.CGGCGGCGAGGCCC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATaaa                                       <  1:628081/100‑1 (MQ=37)                                                                   g.CTGCGCCGAGGCGA.CCCGCCGGGGGCTGCGCCCCCCGGCCCCCCCCCGAGATCTCAGATCCCCCTGTCCTTCGGGCCGGCCGGGCCGAGCGGGTAAAGtc                                    >  2:2021796/1‑100 (MQ=12)                                                                          gcGAGGCCC.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGa                              <  2:702626/100‑1 (MQ=38)                                                                                 gA.CCCGCCGGGGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATTAAGTTCCTCGACCTGGGc                       <  2:2456895/101‑1 (MQ=255)                                                                                       gccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGa                  <  1:539397/96‑1 (MQ=255)                                                                                            gggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCGCCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGt             <  2:527939/101‑1 (MQ=255)                                                                                             ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            <  2:3336273/101‑1 (MQ=255)                                                                                               cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          <  2:584640/101‑1 (MQ=255)                                                                                               cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          >  1:2852572/1‑101 (MQ=255)                                                                                                tGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGa         <  2:1604668/101‑1 (MQ=255)                                                                                                tGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGCCCGa         >  2:2395186/1‑101 (MQ=255)                                                                                                 gcccccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGAt        <  1:902424/98‑1 (MQ=255)                                                                                                   gcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGc      >  1:2157503/1‑101 (MQ=255)                                                                                                   gcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGc      >  2:2386583/1‑101 (MQ=255)                                                                                                    cccccTGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCa     <  1:3065357/101‑1 (MQ=255)                                                                                                    cccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGCCCTGGGCATTGAACAGTCCGATGCa     >  1:4314005/1‑101 (MQ=255)                                                                                                    cccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCa     <  1:1636476/101‑1 (MQ=255)                                                                                                    cccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCa     >  1:2953020/1‑101 (MQ=255)                                                                                                    cccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCa     >  1:3942714/1‑101 (MQ=255)                                                                                                     ccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAg    >  1:3980996/1‑101 (MQ=255)                                                                                                     ccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGATCCTCGACCTGGGCATTGAACAGTCCGATGCAg    >  1:3806409/1‑101 (MQ=255)                                                                                                      cccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAGAGTACCTCGACCTGGGCATTGAACAGTCCGATGCAGc   >  1:3815495/1‑101 (MQ=255)                                                                                                      cccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGc   >  1:2026080/1‑101 (MQ=255)                                                                                                      cccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATACAGc   >  1:971447/1‑101 (MQ=255)                                                                                                       ccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGcc  >  1:3233629/1‑101 (MQ=255)                                                                                                       |                                                                                                     GCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGG.CCGGTCGCCTTGGGGATTTCGCCTC.GG.CTGCGCCGAGGCGA.CCCGCC..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721435‑1721631 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG