New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253892	37 (0.160)	34 (0.150)	2/194	38.2	0.41	intergenic (+50/+41)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2185839	62 (0.260)					intergenic (+112/‑393)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
Rejected: Position hash score below cutoff.

GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG............................................................................................  >  NC_014034/1253794‑1253892 .......................................................................................................GAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTG  <  NC_014034/2185839‑2185752                                                                                                    |||                                                                                          GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                            <  2:3357661/101‑1 (MQ=1) GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                            <  1:2491560/101‑1 (MQ=1) GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                            <  1:560487/101‑1 (MQ=1) GCTGGGCAAGCCCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                            <  1:4101229/101‑1 (MQ=1)  CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                           <  1:1894408/101‑1 (MQ=1)  CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                           <  1:4472112/101‑1 (MQ=1)   cGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.G                                                                                         <  2:3855967/100‑1 (MQ=1)   TGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.G                                                                                         >  2:826320/1‑101 (MQ=1)    GGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gg                                                                                        >  1:3535510/1‑100 (MQ=1)     GGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gga                                                                                       <  2:4385871/101‑3 (MQ=1)     GGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gga                                                                                       <  1:3904558/101‑3 (MQ=1)     GGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Gga                                                                                       >  2:1550662/1‑99 (MQ=1)      GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggag                                                                                      <  2:391647/101‑4 (MQ=1)       tAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagc                                                                                     <  1:2121340/100‑5 (MQ=1)        AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                    <  2:4255640/101‑6 (MQ=1)        AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                    <  2:2834656/101‑6 (MQ=1)        AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagcc                                                                                    >  2:3299303/1‑96 (MQ=1)        AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC.Ggagca                                                                                    >  2:2121190/1‑96 (MQ=1)         AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCC                                                                                    <  2:2022593/101‑1 (MQ=1)         AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCC                                                                                    >  2:1028516/1‑101 (MQ=1)           CTCGGCTTCCAGCCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC                                                                                  <  2:3792155/101‑1 (MQ=1)           CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC                                                                                  >  1:2540634/1‑101 (MQ=1)           CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC                                                                                  <  2:4254239/101‑1 (MQ=1)            TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCG                                                                                 >  2:3379154/1‑101 (MQ=1)              GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAACCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCc                                                                               <  1:2064201/101‑2 (MQ=14)              GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCc                                                                               >  1:487632/1‑100 (MQ=31)                 TTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGG                                                                            >  1:3695250/1‑101 (MQ=32)                 TTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGG                                                                            >  1:294397/1‑101 (MQ=32)                   CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                          >  1:2649444/1‑101 (MQ=32)                   CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                          >  1:4238626/1‑101 (MQ=32)                    CAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCG                                                                         >  2:3707548/1‑101 (MQ=32)                      GACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCC                                                                       >  2:2007560/1‑101 (MQ=32)                           GCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGC                                                                  >  1:2660146/1‑101 (MQ=32)                             TGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCga                                                                >  2:1197148/1‑99 (MQ=32)                                                                                   tacgcCGGGGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGG          >  2:3271817/6‑101 (MQ=40)                                                                                     cgcCGGGGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGC        >  1:601575/4‑101 (MQ=38)                                                                                      gcCGGGGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCC       >  1:2363493/3‑101 (MQ=37)                                                                                         GGGGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCC    >  2:2176261/1‑101 (MQ=35)                                                                                         GGGGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCC    >  2:1784012/1‑101 (MQ=35)                                                                                           GGGTGCGGGGGCGGAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTG  >  1:3252886/1‑101 (MQ=35)                                                                                                    |||                                                                                          GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG............................................................................................  >  NC_014034/1253794‑1253892 .......................................................................................................GAGCCCCCGCAGGGTCGCCTCGGCACCGCCGAGGCGAAACCGCTTTGCACATCAGGCGGCCCCGCCCGGGAGGGAGCGGGGCCGCCTG  <  NC_014034/2185839‑2185752 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG