New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	32 (0.150)	24 (0.110)	4/198	30.4	0.43	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	1253896 =	32 (0.150)					intergenic (+54/+37)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTG  >  NC_014034/392362‑392554                                                                                                       |                                                                                                    ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                                                     <  1:1054498/101‑1 (MQ=255) ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                                                     >  1:3105347/1‑101 (MQ=255) ctccgTGTTACCCCGCTACACTACGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATAGCCCGGGGGTC.GCGGGGCGGAGcccc                                                                                                     <  2:1202450/101‑1 (MQ=25)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg                                                                                              >  2:769280/1‑101 (MQ=255)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg                                                                                              >  1:736046/1‑101 (MQ=255)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg                                                                                              >  1:2471801/1‑101 (MQ=255)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg                                                                                              >  1:1704039/1‑101 (MQ=255)     ttGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg.c                                                                                            >  2:1240050/1‑101 (MQ=255)      tGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg.cg                                                                                           >  1:2642247/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.c...gg.cgg                                                                                          >  1:3517381/1‑101 (MQ=255)          aCCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.Cggggg                                                                                       >  2:1959911/1‑99 (MQ=255)              cgcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.Cgggggggcc                                                                                   >  2:156752/1‑95 (MQ=255)               gcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.Cggggggccgc                                                                                  >  2:2277071/1‑94 (MQ=255)               gcAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.Cggggggccgc                                                                                  >  1:3166499/1‑94 (MQ=255)                 aaGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.Cgggggggcgcgg                                                                                >  2:570466/1‑92 (MQ=255)                    acctgtggggccAAACCGGGAGGGAAATGGGCGGGCCTTTTCATTTTCCCTAAAATACCCGGGGGGCC.CGGGGGCGGACCCCC.C...GG.CGGGTCG.CCTCGgcg                                                                             <  2:2779980/91‑1 (MQ=12)                             cccAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGG.GCCCGgcgcgccgcgggg                                                                   >  2:4065/1‑92 (MQ=18)                              caaaccc.GGAGGAAAAAGGGCAGCCCTTTTCATCTTGCCTAAAATACCCGGGGGGCC.GGGGGGCGGACCCCC.C...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCg                                                                  <  2:2736318/96‑1 (MQ=16)                                       gAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGG.CCCCGGCGCGGCCGGgggggaaaaaac                                                          >  1:2240591/1‑91 (MQ=18)                                        aGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGG.CCCCGGCGCGGCCCCGGCGgaaaacaac                                                         >  2:2111482/1‑95 (MQ=18)                                                   cAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGG.CGCCGGCGCCGCCGCGGCGGGAACAACTGCCGAACCtc.t                                             >  2:15990/1‑101 (MQ=14)                                                             cATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGCG.GCCCGGGGGCGCCCGGGGGGAAACACCTGGCCAACCTC.Tcccccccacc                                   >  1:3145008/1‑94 (MQ=2)                                                                cTTGCCCCAAAAGCCCCGGGGGGCGGGGGGGGGGCCCCCC.C...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCg                                 <  1:1251340/101‑1 (MQ=21)                                                                attctcgcAAAAATCCCGGGGGGG.GGGGGGGGGCGCCCC.CCCGGG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATc                                   <  1:1960037/94‑1 (MQ=16)                                                                        aaaTATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGCG.CCCCGGGGCCGCCGAGGGGGAAAAAACTGCCGGACTTC.TCCCCCCAAACCCgccccccgc                        >  1:4106576/1‑98 (MQ=9)                                                                          atatCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGCG.GCCCGGCGCCGGCGGGGGGGAAACACCTTCCGCACTTCTTCCCCCAAACCAGCCCCCCggcc                       >  2:3848414/1‑99 (MQ=2)                                                                               ccGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGGCCCCCGGGGCGCCCGGGGGGAAA.AACTTTCCGGACTTC.TTCCCCCAAACCCCCCGCCGGGCCcccgc                 >  1:2598675/1‑100 (MQ=0)                                                                                 gggggCC.GGGGGGCCGCCCCCCGC...GGCCGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTCCCGCGt                 <  1:1618841/101‑1 (MQ=25)                                                                                   gggTC.CGGGGGCGGAGCCCC.C...GG.CGGGGGG.GCCCGGGGCAGGCGGGGGGGAAACACCTTCCGAACTTC.TCCCCCAAAACCCGCCCCCCGGCCcccgcccca             >  1:1635740/1‑96 (MQ=9)                                                                                         cGGGGGCGGAGCCCC.C...GG.CGGGGCG.CCCCCGCGCCGCCCAGGCGAAAACACCTGCCCAACTTC.TCCCACAAAACCCGCCCCCCGGGCcgcggccaaccctc        >  2:1832246/1‑91 (MQ=16)                                                                                            gggCGGAGCCCC.C...GG.CGGGGGG.CCCCCGCGCCGCCGCGGGGGAAACACCTGCCGAACTTC.TCCCCCACAACCCGCCCCCCGGCCCGCCCCCAAGCCTCGcc     >  2:36180/1‑100 (MQ=255)                                                                                            gggCGGAGCCCC.C...GG.CGGGGCG.GCCCGGCGCCGCCGCGGGGGAAAAACTTGCCGCACTTC.TCCCCCCAATACCGCCGCCGGCCCCCCGCCCAAGCCTCCct     >  2:3416779/1‑101 (MQ=255)                                                                                             gggcccccccc.g...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGctc    <  2:3068219/94‑1 (MQ=255)                                                                                              ggggcccccc.g...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGctct   <  2:2461004/95‑1 (MQ=255)                                                                                               cGGAGCCCC.C...GG.CGGGGCG.CCCCGGCGCAGCCCGGGCGGAAACAATTGCCGAACTTC.TCCCCCAAAACCCGCCCCCCGCCCCCCGCCCAACATTCCctctc  >  2:2059887/1‑100 (MQ=255)                                                                                                       |                                                                                                    CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACC.GGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCC.C...GG.CGGGTCG.CCTCGGCGCAGCCGAGGCGAAATCACTTGCCGAACTTC.TCCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTG  >  NC_014034/392362‑392554 Base quality scores:  ATCG  < 3 ≤  ATCG  < 21 ≤  ATCG  < 31 ≤  ATCG  < 35 ≤  ATCG  < 41 ≤  ATCG