New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330295	32 (0.140)	49 (0.220)	18/192	20.3	0.60	intergenic (+270/+42)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	2330296 =	32 (0.130)					intergenic (+271/+41)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

TATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....G.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCT  >  NC_014034/2330195‑2330395                                                                                                      |                                                                                                                 tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGGCCCGG.ATCACAGGCGGCCCGGGCGGATTTCACCTGGGGCCAAAGAtcccgggggtccggggg                                                                                                                  >  1:3013816/1‑101 (MQ=255) tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCCGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggggg                                                                                                                  >  1:3782713/1‑101 (MQ=255)  aTTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggc                                                                                                                 <  1:4637802/101‑2 (MQ=255)  aTTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggc                                                                                                                 >  1:1126542/1‑100 (MQ=255)  aTTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggc                                                                                                                 >  1:4748542/1‑100 (MQ=255)  aTTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggc                                                                                                                 <  1:2449561/101‑2 (MQ=255)    ttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcgg                                                                                                               <  2:1345793/101‑4 (MQ=255)    ttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcgg                                                                                                               <  1:1685990/101‑4 (MQ=255)       cgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagc                                                                                                            >  2:1677319/1‑95 (MQ=255)       cgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagc                                                                                                            <  2:2826191/101‑7 (MQ=255)       cgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccggggggccgggggcggagc                                                                                                            >  2:3525327/1‑95 (MQ=255)         ccAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagccc                                                                                                          >  1:472191/1‑93 (MQ=255)         ccAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagccc                                                                                                          >  2:4700359/1‑93 (MQ=255)          cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagcccc                                                                                                         <  2:3926916/101‑10 (MQ=38)          cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagcccc                                                                                                         >  2:3186183/1‑92 (MQ=38)           aaGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagccccc                                                                                                        <  2:964445/101‑11 (MQ=38)                      ggggCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGcc                                                                                       >  2:4538002/1‑101 (MQ=25)                      ggggCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGcc                                                                                       >  2:3432579/1‑101 (MQ=25)                            cgcgggCGGGCCCCCGG.ATCCCGGGCGGCCCGGGC.GCCTTCCCCCGGGGCCAAAAGACCCGGGGGGCCGGGGG....GCGGCCCCCCC.GGCGGGTCGCCGAGGCa                                                                                 <  2:3484496/96‑1 (MQ=9)                               aTGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCg                                                                              <  2:767480/101‑1 (MQ=25)                                gggcgggCCCCGGCACCCCCGGCGGCCCGGGCGGTTTCCCCCGGGGGCAAAAGACCCGGGGGGCCGGGGGG....GGGA..CCCCCGGGCGGGTCGCCGAGGCATCg                                                                              <  2:472147/97‑1 (MQ=255)                                   ggggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTc                                                                          <  1:1852478/101‑1 (MQ=25)                                   ggggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGCGTccgctc                                                                          >  2:3883360/1‑96 (MQ=18)                                     ggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGGGGCGGCGGCTC.gg                                                                       >  2:4418041/1‑101 (MQ=16)                                            g.ATCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATc                                                               <  2:1569853/101‑1 (MQ=21)                                                cccggggggcCGGGGCGGTTTCCACCGGGGGCAAAAGATCCGGGGGGTCGGGGGG....GGGGC.CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATccgt                                                            <  1:4002500/94‑3 (MQ=12)                                                 cccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCtt                                                           <  1:1128621/100‑1 (MQ=21)                                                  ccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGACCGCCCC.CGCGGAAACCCCtt                                                           >  2:1305341/1‑101 (MQ=9)                                                   cggcggCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAg                                                         <  1:3565725/101‑1 (MQ=25)                                                    ggcggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGt                                                        <  1:4327313/101‑1 (MQ=25)                                                      cggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGATCGCCCC.GGC.GAAAACCCCTTGTaa                                                      >  1:2896382/1‑101 (MQ=12)                                                       ggcCGGGGCGGCTTTCACCTGGGGCCAAAGACCCGGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTaaa                                                     <  2:1204711/101‑1 (MQ=21)                                                       ggcCCGGGCGGCTTTCCCCGGGGGCCAAAGATCCCGGGGGTCGGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTaaa                                                     <  2:3384193/101‑1 (MQ=21)                                                        gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAg                                                    <  1:3967738/101‑1 (MQ=25)                                                        gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGCCCCCCTC.CGC.GAACACCCTTCGTaaaa                                                    >  2:2540011/1‑100 (MQ=9)                                                         ccggggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGa                                                   <  2:224891/98‑1 (MQ=21)                                                         ccggggCGGC.TTCCCCCGGGGGCAAAGGACCCGGGGGGCCGGGGG....GCGGA.CCCCCGGGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGa                                                   <  1:2911336/98‑1 (MQ=255)                                                          ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGAACGCCCC.CGCGGAAAACCCtcgtcaaaac                                                   >  1:3262484/1‑92 (MQ=2)                                                           cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGATCGCCCC.GGCGGAAAACCCtcttcaaaaac                                                  >  2:3401721/1‑91 (MQ=9)                                                           cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGCGTCGCCCCGGGG.GAAACCCCTTGTTAAAAAc                                                  >  1:3856951/1‑101 (MQ=9)                                                            gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGCGGCATCGGCTC.GCC.GGACGCCCCTAATAAACAccg                                                >  1:493771/1‑101 (MQ=9)                                                             ggcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgc                                               <  1:3557513/101‑1 (MQ=25)                                                             ggcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgc                                               <  2:4730808/101‑1 (MQ=25)                                                              gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgcc                                              <  2:2817226/101‑1 (MQ=25)                                                               cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgccc                                             <  2:3193896/101‑1 (MQ=25)                                                                ggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGATCGCCCC.CGC.GGAAACCCTTTGTAAAAAacgcccc                                            >  1:784390/1‑100 (MQ=9)                                                                 gcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGAGGGATCGCCCC.CGC.GAAAACCCTTAGTAAAAAacgccccc                                           >  1:4642127/1‑99 (MQ=12)                                                                 gcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCCC.GGC.GAAATCCCTTTGTAAAGAccgcccgc                                           >  1:2296432/1‑101 (MQ=21)                                                                   tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCCCCTC.CGC.GTAAAACCTTACTAAAAAACACCCCCgg                                         >  1:2909700/1‑101 (MQ=9)                                                                    ttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCCGGGGATCGCCCC.CGC.GAAAAACCCTAGTAAAAAacgccccccgg                                        >  1:3726270/1‑96 (MQ=2)                                                                     tCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGCCCGCCCGCGGAc                                       <  1:2561865/101‑1 (MQ=21)                                                                     ccccgtGGGGCAAAAGACCCCGGGGGCCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGAc                                       <  2:2763526/96‑1 (MQ=18)                                                                       aCCGGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAg                                     <  2:4450498/101‑1 (MQ=21)                                                                            gggCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGGCCAGGCCGCGCCCC.CTC.GGAAATCCTTAGTAAAAAACCCCCGCCGACAGGGGTc                                >  1:1537311/1‑101 (MQ=2)                                                                             ggCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATcc                               <  2:3021403/101‑1 (MQ=21)                                                                               ccAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCCC.CGC.GAAAACCCCTAGTAAAAACCGCCCGCGGACAAGGAGCCGa                             >  2:3109316/1‑101 (MQ=12)                                                                                cAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGCTCGCCCC.CGG.GGAAACCCCTAGTAAAGAACGCCCCCGGGCAGGGGTCCGaa                            >  1:2729159/1‑101 (MQ=0)                                                                                cAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGATCGCCCC.GGC.GAAAACCCTTAGTAAAAAACGCCCGCGGGCAGGGATCCgga                            >  2:4675243/1‑99 (MQ=9)                                                                                cAAAGACCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGaa                            <  1:4262192/101‑1 (MQ=21)                                                                                 aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAg                           <  1:1548351/101‑1 (MQ=21)                                                                                 aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCAGAATCGCCTC.GGC.GCAAAGCCCTCTTTATTACCGCCCCCGGACAGGGAGGCGAAg                           >  2:2596258/1‑101 (MQ=0)                                                                                 aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGCTCGCCTC.CGC.GCAAACCCCTTCTAAAAACCCCCCCCGGGGAggggaccgcag                           >  1:1864919/1‑93 (MQ=0)                                                                                 aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCTC.GGC.GAAAACCCTTAGTAAAAAACGCCCGCGGGCAGGGATCCGAAg                           >  1:2147643/1‑101 (MQ=18)                                                                                  aaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGGCGGGGGGTCGCCCC.CGCGGAAACCCCTTA.TAAAAACCGCCCGCGGGCAGGGAGCCGGAgg                          >  1:1042408/1‑101 (MQ=0)                                                                                   aGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGt                         <  2:540983/101‑1 (MQ=25)                                                                                   aGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGATCGCCTC.GGC.GAAATCCCCTAGTAAAAACCCCCCGCGGGCCAGGATCCGCAggg                         >  2:2844906/1‑100 (MQ=9)                                                                                                  gcggg....c.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAcc      <  2:3782478/99‑1 (MQ=255)                                                                                                      g....g.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCt  <  2:2074198/101‑1 (MQ=255)                                                                                                      |                                                                                                                 TATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....G.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCT  >  NC_014034/2330195‑2330395 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG