New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253890	28 (0.140)	43 (0.210)	2/178	34.1	0.50	intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2185844	58 (0.260)					intergenic (+117/‑388)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
Rejected: Position hash score below cutoff.

CCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.GCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCG.CCCCTTTCACCTTG  >  NC_014034/2185746‑2185944                                                                                                       |                                                                                                        ccGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.ccccc                                                                                                       <  1:2436781/101‑2 (MQ=255)  cGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGG.GCG.cccccc                                                                                                      >  2:4145332/1‑99 (MQ=255)  cGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.cccccg                                                                                                      <  2:3877003/101‑3 (MQ=255)       cAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAccc                                                                                                 <  2:3377848/101‑1 (MQ=255)         ggcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAccccc                                                                                               <  1:2555353/101‑1 (MQ=255)          gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                              <  1:4257584/101‑2 (MQ=255)          gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                              <  1:557377/101‑2 (MQ=255)          gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                              <  1:3285711/101‑2 (MQ=255)            ggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGG.GCG.CCCC.CCCccccccccc                                                                                           >  2:1933330/1‑98 (MQ=255)             gcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccggcg                                                                                           <  2:805735/101‑5 (MQ=255)                  gCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCG.GGGGGGG.CCG.CCCC.CCCCCCCCCCGccgggt                                                                                      >  2:319873/1‑96 (MQ=255)                  gCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGGAttt                                                                                     >  2:2888930/1‑101 (MQ=37)                   ttccctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                                    <  1:2073907/100‑1 (MQ=37)                   ctccctccCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                                    <  2:225053/101‑1 (MQ=255)                   ctccctccCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                                    <  1:1990407/101‑1 (MQ=255)                    tccctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTAt                                                                                   <  2:2022875/101‑1 (MQ=255)                     ccctcccGGGCGGGGCCGCCTGATGTGCAAAGGGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATc                                                                                  <  1:1286189/101‑1 (MQ=25)                      cctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATcc                                                                                 <  1:3065749/101‑1 (MQ=255)                      cctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATcc                                                                                 >  1:1734431/1‑101 (MQ=255)                          ccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAg                                                                             <  1:1781537/101‑1 (MQ=255)                           cgggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGa                                                                            <  2:697691/101‑1 (MQ=255)                            gggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGT.CCC.CCCC.CCCCCCCCCGGCGCCTTTTTccccaaaa                                                                           >  1:3658266/1‑96 (MQ=255)                             ggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGCATTTATCCCCAGaaa                                                                          >  2:41047/1‑101 (MQ=25)                               cgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGaaaaa                                                                        <  1:3124769/101‑1 (MQ=255)                                ggggCCGCCTGATGTGCAAAGCGGTTTCGCATCGGCGGTGCCGAGGCGACCCTGCG.GGGGGCC.CCC.CCCC.CCCCCCCCCGCGGCTTTTTTCCCAAAaaaaa                                                                        >  2:2583137/1‑101 (MQ=255)                                 gggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAagc                                                                      <  1:2016186/101‑1 (MQ=255)                                  ggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAagca                                                                     <  1:1508812/101‑1 (MQ=255)                                       ccTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGc                                                                <  1:1784125/101‑1 (MQ=255)                                        cTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCt                                                               >  2:1106948/1‑101 (MQ=255)                                        cTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.CGCCCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCt                                                               <  1:64465/101‑1 (MQ=255)                                         tGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCtt                                                              <  2:4144781/101‑1 (MQ=255)                                             gtgCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.Gccc                                                         <  1:639144/101‑1 (MQ=255)                                               gCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCg                                                       <  2:261506/101‑1 (MQ=255)                                                 aaaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGC.CCG.CCCC.CCCCCCCCCGGCGGATTTATCCCCAGAAAAAACAGCGGCTTCGccccca                                                      >  1:4253265/1‑99 (MQ=255)                                                  aaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAg                                                    <  2:3113970/101‑1 (MQ=255)                                                     cGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGcc                                                 <  1:4225437/101‑1 (MQ=255)                                                     cGGTTTCGCCGCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGcc                                                 <  2:2243179/101‑1 (MQ=37)                                                        tttCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.Tccccccagggcctt                                              >  1:3885566/1‑91 (MQ=21)                                                           cGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGttt                                           <  2:1924428/101‑1 (MQ=255)                                                            gCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGtttt                                          <  2:2471362/101‑1 (MQ=255)                                                             ccTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGttttg                                         <  2:1553172/101‑2 (MQ=37)                                                               tCGGCGGTGCCGAGGCGACCCTGCGGGGGGGCC.CCC.CCCC.CCCCCCCCCCGCGGTTTTTTCCAAAAAAAAAAAAGGGGTTT.CCCCCCCGGCCCTTGttttt                                         >  2:2844254/1‑101 (MQ=255)                                                                   cggTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGca                                  <  2:166896/101‑1 (MQ=37)                                                                   cggTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGca                                  <  1:2978375/101‑1 (MQ=37)                                                                     gTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGcaca                                <  1:2327872/101‑1 (MQ=37)                                                                       gCCGAGGCGCCCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAg                              <  1:403761/101‑1 (MQ=25)                                                                        cctgtgCGTCCTTGC..GGGGGCTCCCC.CCCC.GCA.CCCCCGGCTTATTTATCCCAAGTAAATGCAGCGGCTT.GCCCCTAAGGCCTTG.TTTTGATGGCACAAGa                             <  2:3569230/96‑1 (MQ=16)                                                                         cGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGaa                            <  1:2699962/101‑1 (MQ=37)                                                                          gAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGaaa                           <  1:4188859/101‑1 (MQ=37)                                                                           aGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAAc                          <  2:2249634/101‑1 (MQ=37)                                                                             gCGTCCATGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGc                        <  1:736742/101‑1 (MQ=25)                                                                             gCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGc                        <  2:1172199/101‑1 (MQ=37)                                                                              cGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGcc                       <  1:423110/101‑1 (MQ=37)                                                                               gACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCg                      <  2:287363/101‑1 (MQ=37)                                                                                aCCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGa                     <  2:898529/101‑1 (MQ=37)                                                                                 cccTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAATCGCCGaa                    <  2:917415/101‑1 (MQ=25)                                                                                 cccTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGaa                    <  1:505184/101‑1 (MQ=37)                                                                                   cTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCCTG.TTTTGATGGGACAAGAAAAGCCGaaac                  >  2:3504476/1‑99 (MQ=21)                                                                                    tGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGGAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCg                 <  2:1059854/101‑1 (MQ=25)                                                                                     gC..GGGGGCT.CCG.CCCCAGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.c               >  2:1030281/1‑101 (MQ=37)                                                                                      c..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGACGAACCG.cc              >  2:778582/1‑101 (MQ=25)                                                                                         gggggCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.ccc             <  1:2844461/101‑1 (MQ=37)                                                                                                tccgccccc.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCG.CCCCctttc       <  1:1933459/96‑3 (MQ=37)                                                                                                 ccgccccc.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCa       <  2:815708/97‑1 (MQ=37)                                                                                                     cccc.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCACCtt   <  1:571069/101‑1 (MQ=38)                                                                                                      ccc.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCACCTTg  <  1:869726/101‑1 (MQ=38)                                                                                                      ccc.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGCCCCCTTTCACCTTg  <  2:4164453/101‑1 (MQ=38)                                                                                                       |                                                                                                        CCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.GCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCG.CCCCTTTCACCTTG  >  NC_014034/2185746‑2185944 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG