New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2185845	83 (0.360)	50 (0.220)	22/194	18.6	0.42	intergenic (+118/‑387)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
	?	NC_014034	2330182 =	56 (0.240)					intergenic (+157/+155)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......CG.G.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCC  >  NC_014034/2330090‑2330282                                                                                                             |                                                                                                      cAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGAC.G.......GGCG.......CTCCGCCcccc                                                                                                >  2:4261945/1‑101 (MQ=255)     ggcggcAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGCCCCGGGCGG.......GG.G.......GCCCGCCcccccccc                                                                                            >  1:1612493/1‑98 (MQ=255)       cggcAACGGCGCGCAGAGCGCCGCACGGATCGCCCATTGGCGGGGGGGAATTTCGCCGCGCAGGCGCGGCGACCCGGCCGG.......GG.G.......CCCCGCCcccccacccc                                                                                          >  1:1345885/1‑96 (MQ=255)                   gcAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTgc                                                                                    <  2:216482/101‑1 (MQ=18)                      gagCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGcc                                                                                 <  1:1519482/101‑1 (MQ=18)                       agtgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCa                                                                                <  1:2989077/98‑1 (MQ=18)                       agCGCCGCAGGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCa                                                                                <  2:1982500/101‑1 (MQ=18)                       agCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCa                                                                                <  2:1078889/101‑1 (MQ=18)                        gcgcCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCaa                                                                               <  1:2948450/101‑1 (MQ=18)                        gcgcCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCaa                                                                               <  1:370614/101‑1 (MQ=18)                         cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAg                                                                              <  2:2985986/101‑1 (MQ=18)                          gccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGa                                                                             <  2:407956/101‑1 (MQ=18)                           ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                                                            <  1:1565363/101‑1 (MQ=18)                           ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                                                            <  2:4380998/101‑1 (MQ=18)                            cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                                                           <  1:3752309/101‑1 (MQ=18)                            cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                                                           <  2:75073/101‑1 (MQ=18)                             gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCCCCCCCGGCGTATTTGCGCCAAGaaaa                                                                          <  2:3072877/101‑1 (MQ=18)                              cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                                                         <  2:4751583/101‑1 (MQ=17)                              cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                                                         <  1:2985766/101‑1 (MQ=17)                               aCGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAg                                                                        <  2:3505186/101‑1 (MQ=17)                               aCGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAg                                                                        <  1:33983/101‑1 (MQ=17)                               aCGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAg                                                                        <  1:4113351/101‑1 (MQ=17)                                ctgATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCCGCGTATTTGCGCCAAGAAAAAGc                                                                       >  1:3021591/3‑101 (MQ=12)                                cGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGc                                                                       >  2:2561713/1‑101 (MQ=17)                                   aTCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgg                                                                    >  1:2244136/1‑101 (MQ=17)                                   aTCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgg                                                                    <  1:3114109/101‑1 (MQ=18)                                   aTCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......GG.GGCTCCCCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgg                                                                    <  1:3591565/101‑1 (MQ=18)                                     cGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgggg                                                                  >  1:2826356/1‑101 (MQ=17)                                      ggCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgc                                                                 <  2:1704408/101‑1 (MQ=17)                                      ggCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgc                                                                 <  2:955726/101‑1 (MQ=17)                                      ggCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCCGCGTATTTGCGCCAAGAAAAAGCCGGGgc                                                                 >  2:2040180/1‑101 (MQ=17)                                       gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.A.......CCCCGCACCCCCCGCGGATTTGCGCCAAGAAAAAGCCGGGgcg                                                                >  1:319659/1‑101 (MQ=16)                                         cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                                                              <  2:2920984/101‑1 (MQ=17)                                            tGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                                                           <  1:2800457/101‑1 (MQ=17)                                            gggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCCCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                                                           <  1:1163136/100‑1 (MQ=17)                                               cGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCCGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATTC.g                                                       >  1:1865374/1‑101 (MQ=12)                                                ggAGAGGGAGTTCCCCGCGCAGTGGCGGCGACCCGGGC.G.......GG.GGCTCCCCCCCCGCCCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.gg                                                      <  1:2562424/101‑1 (MQ=9)                                                  agagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.gggg                                                    <  1:961118/101‑1 (MQ=18)                                                  agagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.gggg                                                    <  2:1920136/101‑1 (MQ=18)                                                   gagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGc                                                   <  1:1865929/101‑1 (MQ=18)                                                    agGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGcc                                                  <  2:1863102/101‑1 (MQ=17)                                                     ggAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCCCACCCCCCGCGGATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGccc                                                 >  1:224916/1‑101 (MQ=12)                                                      gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGGGCCG.C.......CCCCCCACCCCCCGCGGATTTGCGCCCAGAAAAAGCCGGGGGGCGCCCGC.GGGGgccc                                                >  2:4456391/1‑101 (MQ=9)                                                      gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCCCACCCCCGGCGCATTTGCGCCAAGAAAAAACCCGGGCGCGCAAGC.GGGGgccc                                                >  2:2450071/1‑101 (MQ=9)                                                         tttCGCCGCGCAGGCGCGGCGACCCGGGC.G.......GG.GGGTCCCCCCCCCCACCCCCCGCGGATTTTCGCCAAGAAAAAGCCGGGGGGCGCATGCGGGGGCCCCgg                                              >  2:488425/1‑101 (MQ=12)                                                          ttCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGAt                                            <  2:4400361/101‑1 (MQ=18)                                                          ttCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGCCGCGCATGC.GGGGCCCCGGAt                                            <  1:3501813/101‑1 (MQ=17)                                                           tCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATc                                           <  1:238832/101‑1 (MQ=18)                                                            cgccgcGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCa                                          >  2:4206489/1‑101 (MQ=18)                                                             gccgcGCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCAc                                         <  2:641983/101‑1 (MQ=18)                                                               cgcgCAGGCGCGGCGACCCGGGC.GGGGGCTCCG.C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACcg                                       <  1:2995793/101‑1 (MQ=18)                                                                                                ggggctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTgg               <  1:2202721/91‑1 (MQ=255)                                                                                                ggggctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTgg               <  1:488476/91‑1 (MQ=255)                                                                                                    ctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGcc           <  2:2972407/95‑1 (MQ=255)                                                                                                     tccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa          >  2:3557294/6‑101 (MQ=255)                                                                                                     tccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa          >  1:1569954/6‑101 (MQ=255)                                                                                                     tccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa          >  1:4246304/6‑101 (MQ=255)                                                                                                     gccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa          <  1:4443109/96‑1 (MQ=255)                                                                                                     cccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa          <  2:2886107/96‑1 (MQ=255)                                                                                                       cgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCaaa        <  1:26003/98‑1 (MQ=255)                                                                                                        gcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAg       <  1:2589226/99‑1 (MQ=255)                                                                                                         cccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGa      <  2:571595/100‑1 (MQ=255)                                                                                                          ccccGCACCCCCGGCTTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt     >  1:4004652/1‑101 (MQ=255)                                                                                                          ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt     <  1:2026644/101‑1 (MQ=255)                                                                                                          ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt     <  2:4278973/101‑1 (MQ=255)                                                                                                          ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt     >  2:691723/1‑101 (MQ=255)                                                                                                            ccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcc   <  1:3696967/101‑1 (MQ=255)                                                                                                             cGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtccc  <  1:1283516/101‑1 (MQ=255)                                                                                                             cGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtccc  <  1:1092329/101‑1 (MQ=255)                                                                                                             |                                                                                                      CAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......CG.G.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGC.GGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCC  >  NC_014034/2330090‑2330282 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG