New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	27 (0.120)	24 (0.110)	2/198	36.0	0.46	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	1253896 =	30 (0.130)					intergenic (+54/+37)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCG  >  NC_014034/392362‑392560                                                                                                        |                                                                                                         ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGcccc                                                                                                          >  1:2945448/1‑101 (MQ=255)     ttGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCc..ggc                                                                                                    >  2:705057/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCc..ggcgg                                                                                                  >  1:3116561/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCc..ggcgg                                                                                                  >  1:634054/1‑101 (MQ=255)         cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCgggg                                                                                                >  1:2018697/1‑100 (MQ=255)               gcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGACTCAAATAT.CCCGGGGGTCC.CGGGGCGGAGCCCCC..GGCGGGGCgagtt                                                                                          >  2:683634/1‑97 (MQ=25)                ggagtctgcgCGGCCAAAGCGGGGGGGACAGTGCCAGCCTATTTCA.CCTACCCTTAAATCC.CCCGGGGGGCG.GGGGGCGGGCCCCCC..GGCGGGTCGCCTCg                                                                                         <  2:2054715/92‑1 (MQ=255)                 aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCgggggggcgcgg                                                                                        >  1:3204842/1‑92 (MQ=255)                 aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGCAC.GGGGGGGGAGCCCCC..GGCGGGGCgtggcgg                                                                                        >  1:3273239/1‑95 (MQ=37)                  aGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCgggggggcccggg                                                                                       >  1:2324663/1‑91 (MQ=255)                      ctggCGGCCCAAACCGGGGGGAAAATGGCAGGCCATTTTC.TCTTGCC.CAAAAATCCCCGGGGGGCCGGGGGGGGGACCCCCC..GGCGGGTCGCCTCGGCGCa                                                                                    <  2:534198/98‑1 (MQ=16)                       tggagccaaaaaCCGGGGGGACACGGGCCGGCTATTTCG.TCTTCCCTCAAAAGC.CCGGGGGGCCC.GGGGGCGCCCCCCCC..GGCGGGTCGCCTCGGCGCAGc                                                                                  <  1:1321046/92‑1 (MQ=12)                               ccaaCCGGGGGGGCAACGTGCGGCCCTTTTATTCTTGCCTAAAATGC.CCGGGGGGTCG.GGGGGGAGGCCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCg                                                                          <  2:2945227/99‑1 (MQ=9)                                                              atcgtccccaaaaTAC.CCGGGGGGCCG.GGGGGCGGGCCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATcc                                        <  2:2169086/91‑1 (MQ=21)                                                                  tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCCCCGCGCCGGCC.GCGCGGAAACACCTGTCG.AACCTCC.CCCCC.ACAACCCgcc                                    >  2:2886642/1‑101 (MQ=2)                                                                  tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGCGGCCCCGCGCCGCCGCGGGGGAAAACCCTTCCCGCAACTTCC.CCCCC.aacccagc                                      >  2:2883971/1‑95 (MQ=2)                                                                           aaaccccGGGGGGCC.GGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGt                              <  2:633986/97‑1 (MQ=25)                                                                            at.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGTGGCCCGGCGCCGCCG.CGGGGGAAAAACCTCACG.AAACTCT.CCCACAAAAACCGCccgccgccccc                           >  2:1290965/1‑96 (MQ=2)                                                                             t.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCCCGGGGCGGCCC.CGGGGGAAACAAATGCCG.AAATTCTCCCCCC.AAACCCGCCCCCCGGCcccc                          >  1:224692/1‑100 (MQ=2)                                                                             accccGGGGGGCG.GGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTcc                            <  2:3204613/99‑1 (MQ=25)                                                                                gggggggGCG.GGGGGGGGCCCCCCGG.GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCcgcg                        <  1:705137/99‑1 (MQ=25)                                                                                   ggggTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCTCCGCGCAGGCC.CGCGGGAAACACTTGCCC.CACCCCT.CCCCC.AAAACCCGCCCCCCGGCCcgccccca                    >  2:3856438/1‑96 (MQ=9)                                                                                            gggggggccccccc..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGc            <  2:3579922/92‑1 (MQ=255)                                                                                            ggggCGGAGCCCCC..GGCGGGGCGCCTCCGCGCCGCCC.CGGCGGAAACACATCCCC.CACTTCT.TCCCC.CAACACCCCCCCCGGCCCCGCGCCCAAACTTCGc            >  2:2568836/1‑101 (MQ=255)                                                                                              gggggccccccg..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGctc          <  1:2128352/94‑1 (MQ=255)                                                                                                cGGAGCCCCC..GGCGGGGCGCCCCGGCGCCGCCC.GGGCGGAAACACTTTCCG.AACTTCT.CCCCC.AAATCCCCCCCCCCGGCCCCCGCCCCAGCTTCGccctc        >  2:4445110/1‑100 (MQ=255)                                                                                                     ccccg..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTc   <  2:2749518/101‑1 (MQ=255)                                                                                                      cccc..GGCGGGCCCCCTCGGCGCAGCCG.AGGCGATATCTCTTGCCG.AACTTCC.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcg  <  1:3814161/101‑1 (MQ=38)                                                                                                        |                                                                                                         CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCG  >  NC_014034/392362‑392560 Base quality scores:  ATCG  < 3 ≤  ATCG  < 16 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG