New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392466	47 (0.200)	62 (0.270)	3/188	27.8	0.53	intergenic (‑114/+29)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	= 3701428	65 (0.270)					intergenic (+5/+44)	grpE/mutS	GrpE protein/DNA mismatch repair protein MutS
Rejected: Position hash score below cutoff.

GTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCA  >  NC_014034/392368‑392566                                                                                                     |                                                                                                        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)                                                                                           gccgcggg.gcggGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTgcgc           <  1:3723228/94‑1 (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)                                                                                                 gg.gcggGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgccg     <  1:672242/100‑1 (MQ=255)                                                                                                 cgagcggGTCCCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgcc      <  1:4813764/98‑1 (MQ=255)                                                                                                 cg.gcggGCCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcgccg     <  2:2369413/101‑1 (MQ=255)                                                                                                    gcggGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCgccgcc   >  2:4188839/1‑101 (MQ=255)                                                                                                     cggGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCNCGTCAAAGCTTCGCTCTGCGCTCGCCGCCa  >  1:1780426/1‑101 (MQ=255)                                                                                                     cggGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCa  <  2:3457094/101‑1 (MQ=255)                                                                                                     |                                                                                                        GTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCC.GGGGGCGGAGCCCCCG.GCGGGTCGCCTCGGCGC.AGCCGAGGCGAAATCACTTGCCGAACT.TCT.CCCACAAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCA  >  NC_014034/392368‑392566 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG