New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330175	32 (0.140)	49 (0.220)	9/200	29.4	0.49	intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	= 3276388	69 (0.310)					intergenic (‑140/+109)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

GACGGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGACGCGGGATCGGGGA  >  NC_014034/3276291‑3276488                                                                                                          |                                                                                                                gacgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCACG.TTTCTTCTCG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCc...ggc                                                                                                           >  2:3555087/1‑101 (MQ=255)    gggggCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.ggg                                                                                                       >  2:468306/1‑101 (MQ=255)    gggggCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.ggg                                                                                                       >  2:3198909/1‑101 (MQ=255)     ggggcaaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.gggg                                                                                                      >  2:1867217/1‑100 (MQ=255)     ggggcaaggggcaaTGCGGCGAAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.gggg                                                                                                      >  2:2976581/1‑100 (MQ=255)          aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.gggggggcc                                                                                                 >  1:2325563/1‑95 (MQ=255)          aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.ggggggccc                                                                                                 >  2:1134030/1‑95 (MQ=255)          aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.ggggggccc                                                                                                 >  2:4199614/1‑95 (MQ=255)          aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGccccg                                                                                                 >  1:4279331/1‑101 (MQ=255)           aggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGCGGGGTcgccc                                                                                                 >  1:505400/1‑100 (MQ=255)                 aaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGgccgcg.cgggg                                                                                         >  1:356045/1‑99 (MQ=255)                 aaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGgccgcg.cgggc                                                                                         >  2:2407293/1‑99 (MQ=255)                     cggcgCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCggcgcg.cggccgcg.c                                                                                    >  2:2793469/1‑101 (MQ=255)                         gcAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCGCC.CGGCCGCg.c.ggc.g                                                                              >  1:1947903/1‑101 (MQ=255)                          gcaccccccccGGGTCACGCCCCCCCGTTTTCTCCTTG.CACC.AAA.AGCGC.GGGGGGGC.G.GG.GGGCGGACCCCCC...GGC.GGGTCGCCGCG.CGGCCGCg.c.ggc.g                                                                              <  1:2813899/96‑1 (MQ=2)                          cagggCCCCCCGGGGACCCGGCCCCCG.TTTCTTCTGG.CCCC.AAA.TCCGC.GGGGGGTC.G.GG.GGGCGGACCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.Ga                                                                             <  2:2901612/98‑1 (MQ=14)                           aaGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGggcgcg.ccggcgcg.ccgggga                                                                              >  1:142661/1‑95 (MQ=17)                           aaGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGGCGCG.GCGCCCCg.c.ggc.ggg                                                                            >  2:4191915/1‑99 (MQ=17)                            aGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGgcgcc.cggccgcc.c.gggggca                                                                            >  1:1249961/1‑96 (MQ=17)                                 ccccGGGCACCCGCCCCCCT.TTTTTTCTGG.CCCA.AAA.TCCGC.GGGGGGCC.G.GG.GGGGGGCCCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAg                                                                      <  1:532993/101‑1 (MQ=9)                                 ccccGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCCCG.CGGGCGCG.G.GGC.GGAACaaaa                                                                      >  1:1749759/1‑100 (MQ=17)                                 ccccGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGGCGCC.CGGGCGCC.C.GGG.GGGACaaaa                                                                      >  1:1195995/1‑100 (MQ=17)                                    cGGGCAAGCCGCCCCCT.TTTTTTTCTG.GGCC.AAA.GGCGG.GGGGGGTCGG.GG.GGGCGCCCCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGga                                                                    <  2:264401/101‑1 (MQ=9)                                     gggCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGGCCCG.CGGGCCCG.C.GGC.GGAAAaaaaaaac                                                                  >  2:1380074/1‑96 (MQ=14)                                      ggCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGGCCCG.C.GGC.GGGACCAAAga.ccc                                                                >  2:3285896/1‑100 (MQ=14)                                        gcaCCGGCCCCCT.TTTTTTTCTG.GCCC.AAA..ACGCGCGGGGGGC.CGGG.GGGGGGGGCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGga.ccga                                                               <  1:4199875/99‑1 (MQ=9)                                          aCCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGGCGCG.CCGGCGCC.C.GGC.GGGACAAAAgaaccgccc                                                             >  2:2866324/1‑94 (MQ=14)                                          aCCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGGCCCG.CGGGCGGG.C.CGC.GCAACaaaacagccacac                                                             >  1:659785/1‑91 (MQ=14)                                           ccGCCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCgg                                                           <  2:4435366/101‑1 (MQ=255)                                            ccgCCCCCT.TTTTTTTCTG.GCCCAAAA.GCCGC.GGGGGGCC.G.GG.GGGCGGCCCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCgg                                                           <  1:1796859/99‑1 (MQ=9)                                                ccccT.TTTTTTTCTG.GCCC.AAAGTCCGC.GGGGGGT..C.GG.GGGCGGGCCCCCCG..GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAg                                                       <  1:2976802/101‑1 (MQ=12)                                                  ccG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCC.C.GGG.GGAACAAAAAA.CCGACCCGGGAGccc                                                    >  1:1884327/1‑101 (MQ=14)                                                   cG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGGC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.GGGGGGGG.G.GGG.GGAACAAAGGG.ACGGCCgggggggggc                                                   >  1:558606/1‑94 (MQ=9)                                                    g.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCCCG.C.GGC.GGAACAAAAGA.CCGACCGGGCGGccccc                                                  >  2:2584330/1‑101 (MQ=18)                                                        tcttctTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCG.C.GGC.GGGACAAAAGA.ACGACCCGGCAGcccccccg                                               >  1:219105/1‑99 (MQ=17)                                                          ttcttGCGCCC.AAA..ACGC.GGGGGGGG.C.GG.GGGGGGGGCCCCCGCGGGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCg                                                <  1:3286128/101‑1 (MQ=16)                                                          ttcttG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCCCG.CGGCCGCG.C.GGC.GCCACAAAAGG.CGCACCCGGCAGGCCCCCCGTc                                             >  2:720099/1‑101 (MQ=14)                                                            cttG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCGCG.CGGGCGGG.C.GGG.GGAAAAAAAAA.AAGACCGGGGGGCCCCCCCGCCgg                                           >  1:2730380/1‑101 (MQ=2)                                                               g.gCCC.AAA.GCCGC.CGGGGGTC.G.GG.GGGCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCa                                        <  2:356010/101‑1 (MQ=255)                                                                      aaa.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCCCG.CGGCCGCG.C.GGC.GGAAAAAAAGA.CCGACCCGGCCGCCCCCCGGGCGGCCCGGG.aa                                  >  1:2055087/1‑101 (MQ=17)                                                                       aaagccGC.GGGGGGGC.G.GG.GGGCGGACCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.aa                                  <  2:2074781/96‑1 (MQ=25)                                                                       aa.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGGCGCGCCGGCCG.G.C.GGC.CGCAAAAAAGA.ACGAACAGGGAGCCCCCCCGTGGGCCacggtac                                  >  2:3710121/1‑95 (MQ=9)                                                                       aa.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGGCGCGCC.GGG.GAAAAAAAGGA..CGACCCGGCAGGCCCCCCGGCCGCCAGAG.AAc                                 >  2:443974/1‑101 (MQ=9)                                                                        a.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCGCG.CGGCCGCG.C.GGCGGAAAAAAAGAA.CGGACGGGGCGGCCCCCCGGCGGGCCGGGG.AAc                                 >  2:4171592/1‑101 (MQ=9)                                                                              c.cGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCG.C.CGC.GGAACAAAAGA.CCCACCCGGCCGCCCCCCCGGCGGCCCGTG.GAcccccaa                           >  2:1787358/1‑97 (MQ=17)                                                                                ggggggAC.C.GGTGGGCGGCGCCCCG...GGC.GAGTCGCCGCG.CGGCCGCG.C.AGC.GAAACAAAGGA.CCGCCCGGGCAGCCCCCCGGTCGGACAGTG.AACCCGaaa                           <  1:2533858/100‑1 (MQ=25)                                                                                ccgatctC.C.GG.GGGCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAAc                          <  2:935339/95‑1 (MQ=255)                                                                                 gggggTC.G.GG.GGGCGGAGCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAAcg                         <  1:2866927/101‑1 (MQ=255)                                                                                   gggTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGGCGCG.C.GGC.GGAACAAAAGA.CCGACCGGGCCGCCCCCCCGGCGGCCCGGG.GACCCGAAAcgcg                       >  2:2439999/1‑101 (MQ=21)                                                                                   gggTC.C.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCG.G.CGC.GGAACAAAAGG.ACGACGACGGCGGCCCCCGGCCGGCCCGCGAAACCCGaaagcc                        >  2:1031790/1‑98 (MQ=2)                                                                                     gggccggg.gggCGGGGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAAcgcg                       <  2:4279062/95‑1 (MQ=255)                                                                                      tC.C.GG.GGGCGGAGCCCCC...GGC.GGGGAGCCCCG.CGGGCGCG.C.GGC.GGAAAAAAAGA.CCCACCGGGCAGCCCCCCCGGCGGCCAGCG.AACCCCAAAccagcag                    >  1:1752847/1‑95 (MQ=16)                                                                                       c.c.GG.GGGCGGAGCCCCC...GGC.GGGGGGCCCCG.CGGCCCCG.CGGGG.GAAAAAAAGAA.CCACCCGGGGGGCCCCCCGGCCGGCCGGGG.AACCCGaaaacaaagg                    >  1:935424/1‑94 (MQ=12)                                                                                       c.c.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CCGCCGCG.C.GGG.GGAACCAAAGA.CCCACCGGGCCGGCCCCCCGTCGGGCCGTGCACCCCGAAAccgcagg                    >  2:3910997/1‑95 (MQ=12)                                                                                       c.c.GG.GGGCGGAGCCCCC...AGC.GGGTCGCCGCG.CGGGCGCG.A.GGG.GGAACAAAAAAGCAGAAAGGG.AGCCCCCCCCACGGACAGTG.AACACCAAACGCCA.Agg                  >  2:3674409/1‑101 (MQ=9)                                                                                         c.GG.GGGCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCCGGGAGGCCCCCCGGCGGCCCGGG.AACCCCAAACGCGA.Aggg                 >  1:1858636/1‑101 (MQ=21)                                                                                          ggg.gggCGGCCCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.Aggg                 <  2:142640/100‑1 (MQ=255)                                                                                           gg.gggCGGCCCCCCG...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGa                <  1:1867341/101‑1 (MQ=255)                                                                                           gg.gggCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GGAACAAAAGA.CCGACCGGGGCGCCCCCCCGGCGGCCAGCG.AACCCCCAAAGCGA.Aaggg                >  2:2564237/1‑100 (MQ=18)                                                                                           gg.gggCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGGCGCG.C.CGC.GGAAAAAAAGA.CCGACCGGGCAGCCCCCCCGTCGGCCCGCG.AAACCCAAACGCGA.Agggg                >  2:435448/1‑100 (MQ=21)                                                                                           gg.gggCGGACCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGa                <  1:2407450/101‑1 (MQ=255)                                                                                            ggggcgcgccccccg...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGa                <  2:3218035/91‑1 (MQ=38)                                                                                             ggggcagccccccc...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGAc               <  2:4326612/92‑1 (MQ=255)                                                                                              gggCGGAGCCCCC...GGC.GGGGCGCCGCG.CGGCCGCG.C.GGC.GGAAAAAAAGA.CCGACCGGGCAGGCCCCCCGGCGGGCCGGG.AACCCGAAAAGCGA.AAGGGcg              >  2:3962460/1‑101 (MQ=16)                                                                                               gcgggccgcccg...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGAcgc             <  1:3199138/93‑1 (MQ=255)                                                                                                   gAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGACGCGGGa         <  2:1947774/101‑1 (MQ=255)                                                                                                       cccc...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGACGCGGGATCgg     <  1:2793675/101‑1 (MQ=255)                                                                                                       cccc...GGC.GGGGCGCCGCG.CGGCCGCG.C.GGC.GCAACAAAGGA.CCCACCGGGCCGCCCCCCGGTCGGCCCGGG.GACCCCCAAAGCGAGAGGGA.GCgggggcgg     >  2:1262095/1‑96 (MQ=255)                                                                                                          c...ggc.ggGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGACGCGGGATCGGGGa  <  1:1103290/101‑1 (MQ=255)                                                                                                          |                                                                                                                GACGGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCG.TTTCTTCTTG.GCCC.AAA.TACGC.CGGGGGTC.C.GG.GGGCGGAGCCCCC...GGC.GGGTCGCCGCG.CGGCCGCG.C.GGC.GAAACAAAGGA.CCGACCGGGCAGCCCCCCGGTCGGCCAGTG.AACCCGAAACGCGA.AGGGACGCGGGATCGGGGA  >  NC_014034/3276291‑3276488 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG