New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	33 (0.140)	26 (0.110)	2/198	38.6	0.43	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	1253896 =	37 (0.160)					intergenic (+54/+37)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCC  >  NC_014034/392362‑392562                                                                                                      |                                                                                                           ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGcccc                                                                                                            <  1:1913759/101‑1 (MQ=255)  tcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATTCCGGGGGTC.CGGGGGCGGAGccccc                                                                                                           >  2:4345039/1‑101 (MQ=255)  ccctTGCCACCGCGCAAGACTAGGCGGCCAAAACCGGAGGGAAAAGGGCAGGCCATTTCATCTTGCCTAAAATACCCGGGGGGCC.GGGGGGGGGACccccc                                                                                                           <  2:3883475/100‑1 (MQ=255)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc.gg                                                                                                        >  1:3867400/1‑101 (MQ=255)      tGTAACCGCGCAAGCCTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTAATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGGGCCCCc.ggcg                                                                                                      >  2:4633304/1‑101 (MQ=37)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCc.ggcgg                                                                                                     >  2:3726055/1‑101 (MQ=255)        tCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCggg                                                                                                    >  2:2232111/1‑101 (MQ=255)         cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggg                                                                                                   >  2:1271841/1‑100 (MQ=255)          aCCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCggggg                                                                                                  >  1:308611/1‑99 (MQ=255)           ccGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggggg                                                                                                 >  1:1213021/1‑98 (MQ=255)                 aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCgggggggcggtg                                                                                           >  2:85766/1‑92 (MQ=255)                           ggCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGCGGCCCGGGG.CCGccccg                                                                                >  1:2819665/1‑98 (MQ=21)                                aaaCCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.GCGCCGCGGCgga                                                                           >  2:4451234/1‑99 (MQ=18)                                         ggaacagggCCGGCCCTTTCCTTTTTCCCAAAACTTCCCGGGGGGCGGGGGGGGGGCCCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTg                                                                  <  2:2648149/94‑1 (MQ=9)                                              aTGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCCGCG.CCGGCGAGGGGGAAACA.catacccaaa                                                            >  2:3105023/1‑92 (MQ=14)                                                       cATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCTCGGCG.CCGCCCAGGCGGAAAAA.CATTCCCGACTTCT.ccccc                                                  >  2:2872107/1‑99 (MQ=17)                                                                    cTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCTCGGCG.CCGCCGGGGGGGAAAAA.CTTTCCGCACCTCT.CCCCCCCACCCCg.ccg.cc                                   >  2:3434921/1‑101 (MQ=9)                                                                     tCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.GGGGCGCGGCGGAAACACCTTCCCGACCTTTC.CCCCCAAACCCGc.ccc.cc                                   >  1:3489145/1‑101 (MQ=2)                                                                         atatCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGCG.CGGCCGCGGGGGAAACA.CTTTCCCAACCTCT.CCCCCCAAACCCG.CCC.CCGGCcc                              >  1:514642/1‑101 (MQ=9)                                                                          atccccGGGGGGC.CGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTcc                              <  1:2013339/98‑1 (MQ=37)                                                                          acccgggggggCC.GGGGGGCGGGCCCCCCGGGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTcc                              <  1:2004951/95‑1 (MQ=25)                                                                             cgggggggGC.GGGGGGGGGGCCCCCC.GGCGGGGCGCCGCGGCG.CACCCGAGGCGAAATCC.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCcgcg                          <  1:656657/98‑1 (MQ=255)                                                                                tctggTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCa                       <  2:2196329/98‑1 (MQ=255)                                                                                gggggTC.CGGGGGCGGAGCCCCC.GGCGGGGCGCCCCCGCG.CCGCCCGGGGGGAAACA.CTTGCCGAACCTCTCCCCCCAAACCCGC.CCC.CCGGCcccccccc                        >  1:3024107/1‑96 (MQ=9)                                                                                 gcgggggcGGGGGCGGCCCGCCG.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTCCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCa                       <  1:4364068/94‑1 (MQ=25)                                                                                  gggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGGG.CGGCCCCGGGGGGAACA.CCTTCCGGACCTCT.CCCCCACAACCGG.CCC.CCGGCGCcgccgccca                     >  1:4631728/1‑95 (MQ=2)                                                                                  gggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGCG.CCGCCGGGGGGGAAAAA.CTTGCCGCACTTCT.CCCCCAAAACCCG.CCG.CCCGGCCCGCGCCaaa                     >  2:3098596/1‑101 (MQ=16)                                                                                   ggTC.CGGGGGCGGAGCCCCC.GGCGGGGTGGCCCGGGG.CACGCGCGGCGCAAACA.ATTGCCCACCCGCT.CCCCCCAATACCG.CCG.CCGGTCCCCCGCCCAAg                    >  1:4446381/1‑101 (MQ=2)                                                                                   ggTC.CGGGGGCGGAGCCCCC.GGCGGGGGGCCCCGGGG.CCGCCCCGGGGGAAACA.CCTGCCCAACTTCT.CCCCCCAAACCCG.CCG.CCCGGccccccgccaca                    >  1:2196479/1‑92 (MQ=9)                                                                                     tC.CGGGGGCGGAGCCCCC.GGCGGGGGGGCCCGGCGCCGGCCGGGGGGAAACAA.CTT.CCGCACTTCT.CCCCCCAAACCGC.CCG.CCCGGCCcgccgccaaacc                  >  2:3357613/1‑92 (MQ=255)                                                                                      c.cGGGGGCGGAGCCCCC.GGCGGGGGGCCCCCGCG.CCGCCCCGGCGGAAACA.CCTGCCGAAACTCT.CCCCCAAAACCCG.CCGCCCGGTCCC.CGCCAAAggct                 >  2:3086984/1‑98 (MQ=255)                                                                                         gggggCGGAGCCCCC.GGCGGGGCGCCTCCGCG.CGGCCCCGGGGGAAACA.CTTTCCGCACTTCT.CCCCCCAAACCGGCCCC.CCGGCCCCCCGCCAAAGCTTc                >  2:2791014/1‑101 (MQ=255)                                                                                          ggggGGGCGCCCCCGGGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCg               <  2:4622736/101‑1 (MQ=37)                                                                                            ggCGGAGCCCCC.GGCGGGAAGCCTCCGCG.CAGCCCAGGCCAAATAA.CTTGCCGAGCCTCT.CCCCCACATCCGG.ACG.CCGGGCCCCCGGCACAGCTGCGctc            >  2:3408885/1‑101 (MQ=255)                                                                                              cGGAGCCCCC.GGCGGGGGGCCCCCGGG.CCGCCGGGGGGGAAAAA.ATTGCCGAAATTTT.CCCACCAAACCCG.CCC.CCCGTCCCCCGCCAAAGACTCGcgcct          >  2:3678130/1‑97 (MQ=255)                                                                                                      cc.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgcc  <  2:1419788/101‑1 (MQ=255)                                                                                                      |                                                                                                           CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCC  >  NC_014034/392362‑392562 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG