New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	60 (0.250)	33 (0.140)	2/198	29.6	0.41	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	1253896 =	36 (0.150)					intergenic (+54/+37)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTC  >  NC_014034/392362‑392559                                                                                                      |                                                                                                      ctcctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGcccc                                                                                                       >  2:4596937/1‑101 (MQ=255)   cctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg                                                                                                     >  2:478885/1‑101 (MQ=255)    ctTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGGCC.GGGGGCGGAGCCCCcg.g                                                                                                   >  2:4387982/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg.gcgg                                                                                                >  2:794720/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg.gcgg                                                                                                >  1:2369577/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg.gcgg                                                                                                >  2:4456662/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg.gcgg                                                                                                >  2:3722950/1‑101 (MQ=255)       gTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCcg.gcgg                                                                                                >  1:4376220/1‑101 (MQ=255)        tCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggg                                                                                               >  2:2723951/1‑101 (MQ=255)         cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCgggg                                                                                              >  2:4651312/1‑100 (MQ=255)         cACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCgggg                                                                                              >  2:2125712/1‑100 (MQ=255)          aCCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggggg                                                                                             >  1:4419118/1‑99 (MQ=255)             gcgcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCgggcccgc                                                                                          >  2:152062/1‑96 (MQ=255)              cgcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCgggggggcg                                                                                         >  1:4447531/1‑95 (MQ=255)               gcAAGACTATGCGGCCCAAACTGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGtgggacg                                                                                        >  2:1294305/1‑95 (MQ=255)               gcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggggtgcggc                                                                                        >  2:884524/1‑94 (MQ=255)               gcAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCgggggggggc                                                                                        >  2:2833849/1‑94 (MQ=255)                cAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggggggcgcgg                                                                                       >  2:1976683/1‑93 (MQ=255)                cAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggggggccccc                                                                                       >  1:4561980/1‑93 (MQ=255)                 aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCggggtgcgacgg                                                                                      >  1:4648339/1‑92 (MQ=255)                 aaGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCCGAGGCCCCG.GGGGGtgagggtgg                                                                                      >  2:4701251/1‑93 (MQ=25)                        tGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGGCTCGGGGC.GGcc                                                                              >  2:3369035/1‑101 (MQ=21)                          cGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCCCCgcgccccggc                                                                             >  1:4616561/1‑95 (MQ=21)                              ccAAACCGGAGGGACAATGGCATGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCGCGGCGC.GGCCGCGGCg                                                                        >  1:3293376/1‑101 (MQ=21)                                   cgggAGGGACAATGGCGGGCCATTTCATCTTCCCAAAAATACCCGGGGGGCCG.GGGGGGGGACCCCCGG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATc                                                                   <  2:848929/99‑1 (MQ=21)                                   ccGGGGGGGAAATGGGGGGCCGTTTTCACTTGCCACAAAACACCCGGGGGGCCGGGGGGCGAACCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAAt                                                                    <  2:691883/101‑1 (MQ=9)                                      gAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGGCGCGGCGC.CGCCGGgggggagaaaac                                                                >  2:1321492/1‑91 (MQ=18)                                               tGGCAGCCATTTTCACCTTGCCGCAAAT.CCCGCGGGGCCC.GGGGGGCGAGCCCCCGTGCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACt                                                       <  2:664299/101‑1 (MQ=16)                                                        aTTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGCGCCTCGGCGC.AGCCGCGGCGGAAAAACTTCCCGAACT.TCT.cccccc                                            >  1:3632404/1‑98 (MQ=18)                                                          ttCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCCCGGGGG.GGCCCGGGGGGAAACACCTTCCCAGCT.TCT.ccccccaa                                          >  1:4528211/1‑96 (MQ=2)                                                          ttCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCCCCGCGC.GGCCCGGGGGGAAACACCTGCCCCACT.TCT.CCcccaca                                          >  2:1118169/1‑99 (MQ=9)                                                            cATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGGCCCCGGGC.CGCCGGGGCGGAAAAACCTGCCGCAAT.TCC.ccccccaaac                                        >  1:2676976/1‑94 (MQ=2)                                                            cATCTTGCCAAAAATGCCGCGGGGGTCG.GGGGGCGGGCCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATc                                        <  2:1515788/101‑1 (MQ=25)                                                             tttttcccaaaaaTACCCGGGGGGCCG.GGGGGCGGCCCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATcc                                       <  2:3293114/91‑1 (MQ=21)                                                             ttCTTGCCTAAAATACCCCGGGGGGCG.GGGGGCGGGCCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATcc                                       <  2:828381/100‑1 (MQ=37)                                                               cTTGCCTAAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGGCCCGGGGG.CGCCGAGGCGCAAAACCATGCCGCAAT.TCT.CCcccacctcccc                                     >  1:683996/1‑94 (MQ=2)                                                                 tGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGCGCCCCCGGGC.GGCCGGGGGGGAAACCATTGCCCAACT.TCT.CCCCCCAATcccccc                                   >  2:2342452/1‑97 (MQ=9)                                                                  gCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGTGCCTCCGGGC.CGCCGCGGCGGGAAGACCTGCCGCACC.TCT.CCCCCCAAACCCgccc                                  >  2:2285319/1‑100 (MQ=9)                                                                   ccTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGGCCCGGCGC.GGCCGCGGGGGAAAAACCTTTCGAAAA.TCT.CCCCCAAAAACCgccgc                                 >  1:1611045/1‑101 (MQ=2)                                                                      cAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCTCCGCGC.GGCCCCGGCGGGAACACCTGCCCCCCT.CCT.CCCACCAACccccacgcccg                              >  2:219322/1‑92 (MQ=2)                                                                         atatCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCTCGGCGC.CGCCGAGGCGGAAAAACCTGCCCCACC.TCT.CCCCCACAAACCgccgcccggcc                           >  2:3030775/1‑96 (MQ=9)                                                                          tatCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCCCCGCGC.CGCCGCGGGGGAAAAACATGCCGCACC.TCT.CCCCCACAAACCGCCGCCCGGccc                          >  1:704144/1‑101 (MQ=2)                                                                               cGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGCGCCCCGGGGC.GGCCCCGGGGGAAAAACCTTCCGCACT.TTTCCCCCCAAACCCGCCCCCCGGCccccgcc                      >  1:3044559/1‑97 (MQ=2)                                                                               cGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGGCGCCCCCGCGC.CCCCGGGGGGGAAACACCTGCCGCACT.TCT.CCCCCCAAACCCGCCCCCCGCcccccccc                     >  2:4474409/1‑96 (MQ=9)                                                                                gggggTCC.GGGGGCGGAGCCCCCG.GCGGGGGGCCCCGGCGCGGGCCGGGGGGAAA.CACCTGCCCAAAC.TCT.TCCCCAAAACCCGCCCCCGGGCCcccgccc                    >  2:2815870/1‑98 (MQ=2)                                                                                  gggTCC.GGGGGCGGAGCCCCCG.GCGGGGCGCCCCGGGGC.CGCCGGGGCGGGAACACCTTCCGCACT.TCT.CCCCCCAAACCCGCCCCCCGCcccccccccca                  >  1:3810702/1‑93 (MQ=2)                                                                                      cc.GGGGGCGGAGCCCCCG.GCGGGGCGCCCCCGCGC.CGCCCCGGGGAAAACAACTTCCCCACC.TCT.CCCCCCAAACCCGCCCCCGGGCCcgccgccaaaccc              >  2:3963390/1‑91 (MQ=2)                                                                                       cggggggGGGGCCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCtt              <  2:1517881/99‑1 (MQ=255)                                                                                       c.GGGGGCGGAGCCCCCG.GCGGGGCGCCTCGGCGC.CGCCGAGGGGAAAAAACTTGCCGAACT.TCT.CCCACAAAAACAGCCGCCCGGCCCGCGCCACAACTTc             >  2:1104705/1‑101 (MQ=255)                                                                                         gggggggcccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTTCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCg            <  2:3942304/91‑1 (MQ=37)                                                                                         gggggggcccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCg            <  1:4456981/91‑1 (MQ=38)                                                                                          gggccgcccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGc           <  1:394697/92‑1 (MQ=38)                                                                                            ggggcccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGctc         <  1:4152946/94‑1 (MQ=255)                                                                                               ggAGCCCCCG.GCGGGTAGGCCCGGCGC.AGCCGGGGCGAAATCATTTACCGAACTGTTT.CCCACAAA.CCGACGGCCGGCCGCCCCTCGAAGGTTCGcgcctg      >  2:666980/1‑96 (MQ=255)                                                                                               gcggCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTgc      <  2:4142428/98‑1 (MQ=255)                                                                                                ggcccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTgcg     <  2:4870560/98‑1 (MQ=255)                                                                                                cccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTgcg     <  1:1112193/98‑1 (MQ=255)                                                                                                cccccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCAAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTgcg     <  1:4701574/98‑1 (MQ=255)                                                                                                  ccccccG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCt   <  2:704055/100‑1 (MQ=255)                                                                                                   ccccgG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTc  <  1:2522193/101‑1 (MQ=255)                                                                                                   cccccG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTc  <  2:2287936/101‑1 (MQ=255)                                                                                                      |                                                                                                      CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTC  >  NC_014034/392362‑392559 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG