New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253892	42 (0.150)	47 (0.170)	3/194	41.9	0.44	intergenic (+50/+41)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2185839	78 (0.270)					intergenic (+112/‑393)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
Rejected: Position hash score below cutoff.

TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG..............................................................................................  >  NC_014034/1253793‑1253892 ........................................................................................................GAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTGT  <  NC_014034/2185839‑2185751                                                                                                     |||                                                                                            TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGG                                                                                               <  1:3721486/101‑1 (MQ=1)  GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                              <  1:1648087/101‑1 (MQ=1)  GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                              >  2:3610669/1‑101 (MQ=1)   CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTACATACCTCGGGGGTGCGGGGGC                                                                                             <  1:3287476/101‑1 (MQ=1)   CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                             <  2:5495142/101‑1 (MQ=1)    TGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.G                                                                                           <  2:2879266/101‑1 (MQ=1)     GGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gg                                                                                          <  1:2768421/101‑2 (MQ=1)      GGCAAGCTCGGCTTCCAGGCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gga                                                                                         <  1:4407218/101‑3 (MQ=1)        CAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                       >  2:5655651/1‑97 (MQ=1)        CAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                       >  2:4540525/1‑97 (MQ=1)        CAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                       >  2:4237004/1‑97 (MQ=1)        CAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                       <  2:2296930/101‑5 (MQ=1)        CAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                       <  1:604756/101‑5 (MQ=1)         AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                      >  2:4611253/1‑96 (MQ=1)         AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                      <  2:2659941/101‑6 (MQ=1)         AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGGGCGGGGGC.Ggagcc                                                                                      >  1:5707759/1‑96 (MQ=1)         AAGCTCGGCTTCCAGACCGGCTGAGCCTTGGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                      <  1:1623746/101‑6 (MQ=0)          AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCC                                                                                      <  2:184310/101‑1 (MQ=1)          AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCC                                                                                      >  1:5609830/1‑101 (MQ=1)           GCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC                                                                                     >  1:867335/1‑101 (MQ=1)            CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAACCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC                                                                                    <  2:3528109/101‑1 (MQ=1)            CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCa                                                                                    <  1:620523/101‑2 (MQ=1)            CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC                                                                                    <  2:5185018/101‑1 (MQ=1)            CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.GGGCCCacc                                                                                   >  2:1269995/1‑98 (MQ=0)             TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.G                                                                                  >  2:650778/1‑101 (MQ=1)             TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.G                                                                                  >  1:3619821/1‑101 (MQ=1)             TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.G                                                                                  >  1:3367476/1‑101 (MQ=1)               GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCc                                                                                >  2:3521661/1‑100 (MQ=31)                GCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCcg                                                                               >  1:2245452/1‑99 (MQ=32)                GCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACAGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCcg                                                                               >  2:3983219/1‑99 (MQ=17)                  TTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGG                                                                             >  2:3554826/1‑101 (MQ=32)                    CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGgc                                                                           >  1:1740969/1‑99 (MQ=17)                    CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTC                                                                           >  1:2161639/1‑101 (MQ=32)                     CAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCG                                                                          >  2:5610371/1‑101 (MQ=32)                      AGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGC                                                                         >  2:3142334/1‑101 (MQ=32)                          CGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGCCTCG                                                                     >  1:3789821/1‑101 (MQ=32)                            GCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGCCTCGGC                                                                   >  2:3296169/1‑101 (MQ=32)                            GCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGCCTCGGC                                                                   >  2:5611123/1‑101 (MQ=32)                             CTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGCCTCGGCg                                                                  >  2:3316840/1‑100 (MQ=32)                             CTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC.GCCGGGTCGCCTCGGCg                                                                  >  1:5399599/1‑100 (MQ=32)                                                                                     acgcCGGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGG          >  1:3308361/5‑101 (MQ=39)                                                                                       gcCGGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCC        >  1:4476191/3‑101 (MQ=37)                                                                                        cCGGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCG       >  1:2568240/2‑101 (MQ=35)                                                                                        cCGGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCG       >  2:4473393/2‑101 (MQ=35)                                                                                         CGGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGC      >  2:669640/1‑101 (MQ=35)                                                                                          GGGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCC     >  2:4234162/1‑101 (MQ=35)                                                                                           GGGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCT    >  1:725627/1‑101 (MQ=35)                                                                                           GGGGTGCGGGGGC.GCGCCCCCGGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCT    <  2:3209135/101‑1 (MQ=255)                                                                                            GGGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTG   >  1:5409499/1‑101 (MQ=35)                                                                                             GGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTGT  >  1:2351044/1‑101 (MQ=35)                                                                                             GGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTGT  >  2:3082272/1‑101 (MQ=35)                                                                                             GGTGCGGGGGCGGAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTGT  >  1:3980354/1‑101 (MQ=35)                                                                                                     |||                                                                                            TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG..............................................................................................  >  NC_014034/1253793‑1253892 ........................................................................................................GAGCCCCC.GCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTGT  <  NC_014034/2185839‑2185751 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG