New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392466	29 (0.130)	44 (0.200)	6/188	33.1	0.55	intergenic (‑114/+29)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	= 3701428	44 (0.190)					intergenic (+5/+44)	grpE/mutS	GrpE protein/DNA mismatch repair protein MutS
Rejected: Position hash score below cutoff.

TGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCA  >  NC_014034/392367‑392566                                                                                                      |                                                                                                          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)                                                                                                cggggccggGTCGCCTCGGCG.CAGCCGAGGCGAAATCC.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcg        <  1:85780/95‑1 (MQ=255)                                                                                                 cc.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgcc      <  2:1419788/101‑1 (MQ=255)                                                                                                  cgggcggGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgcc      <  1:4160217/99‑1 (MQ=255)                                                                                                     gcggGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCgccgcc   >  1:2908911/1‑101 (MQ=255)                                                                                                      cggGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCCCTCGCCGCCa  >  1:917461/1‑101 (MQ=255)                                                                                                      |                                                                                                          TGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTC.CGGGGGCGGAGCCCCC.GGCGGGTCGCCTCGGCG.CAGCCGAGGCGAAATCA.CTTGCCGAACTTCT.CCCACAAATCCGG.CCG.CCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCA  >  NC_014034/392367‑392566 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG