New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330175	32 (0.130)	38 (0.160)	5/200	35.3	0.43	intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	= 3276388	68 (0.290)					intergenic (‑140/+109)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

CACGACGGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGACGCGGGATCGGGG  >  NC_014034/3276288‑3276487                                                                                                         |                                                                                                        cACGACGGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...ccccc                                                                                                         <  2:4104292/101‑1 (MQ=255)  acgacgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCc.g                                                                                                       >  1:107893/1‑101 (MQ=255)    gacgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCNGGGGCG.GAG...CCCCc.ggc                                                                                                     >  2:910041/1‑101 (MQ=255)    gacgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCc.ggc                                                                                                     >  1:1933236/1‑101 (MQ=255)     aggggggCAAGGGCCAATGCGGCGCAGGGCCCCCGGGGCACCCGCCCCCCGTTTCTTCTTGGCCCAAATCCGCCGGGGGTCCGGGGGCG.GAG...CCCCc.ggcg                                                                                                    <  2:1690405/99‑1 (MQ=18)     acgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCc.ggcg                                                                                                    <  2:2782781/101‑1 (MQ=255)      cgGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCc.ggcgg                                                                                                   <  2:2955812/101‑1 (MQ=255)       gggggCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCggg                                                                                                  >  1:700841/1‑101 (MQ=255)        ggggcaaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCgggg                                                                                                 >  2:3588528/1‑100 (MQ=255)           gcaaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCggggggg                                                                                              >  2:1702047/1‑97 (MQ=255)            caaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCggggggcc                                                                                             >  1:2003433/1‑96 (MQ=255)             aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCggggggcgg                                                                                            >  2:4205194/1‑95 (MQ=255)             aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCggggggcgc                                                                                            >  2:3931552/1‑95 (MQ=255)             aaggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGCTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGAcg.cgg                                                                                           >  1:1210013/1‑99 (MQ=255)               ggggcaaTGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCgggggggccgg                                                                                          >  2:1920530/1‑93 (MQ=255)                           cgcAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.Ccg.cgcggccccccggc                                                                            >  1:1564968/1‑101 (MQ=18)                            gcAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCG.CGCGGGCCCgccgcg                                                                           >  2:344373/1‑101 (MQ=18)                               aGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCG.CGCGGCCGCccggcggca                                                                        >  1:2786348/1‑98 (MQ=17)                                gcccccccGGGCACCCGCCCCCCTTTTCTTCTGGCCCAAAATCCGCGGGGGGCCGGGGGGCG.GAC...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAAc                                                                       <  1:2971976/99‑1 (MQ=14)                                 cccccccGGCGCACCCCCCCCCTTTTTCTCCTGGCCAAAATCCCGGGGGGGGCCGGGGGGC.GCG...CCCCCGGGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAAc                                                                       <  2:212277/100‑1 (MQ=2)                                       cGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.GCC.CCGGGCCGGGCGGGGGAACAAAAgaa                                                                >  1:2480594/1‑100 (MQ=14)                                        tcccacccGGCCCCCGTTCCTTTTGGGCCAAAACCCCCGGGGGGCCCGGGGGCG.GGC...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGgacc                                                               <  1:3106129/95‑1 (MQ=9)                                        gggCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCC.CGCGGGCCCGCGGGGGAACCAACgacc                                                               >  1:1563690/1‑101 (MQ=14)                                        gggCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CGCCGCCGCCCCGCGGGACAAAAgacc                                                               >  1:783978/1‑101 (MQ=14)                                        ccgcgccccccccccCTTTTTTCTTCGCCCCAAAAGCCCGGGGGGGGGGGGGGG.GGGCCCCCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAgg                                                                  <  1:370496/91‑1 (MQ=2)                                         ggCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.GCC.CCCGGGCGCGCGGCGGAACAAAAgaacc                                                              >  2:3623163/1‑98 (MQ=17)                                          ccccccGCCCCCCTTTTCCTTCTGCCCCAAACCCGGGGGGGGGGGGGGGGGG.GCC...CCCCCGGGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGgacc.g                                                             <  1:1155547/97‑1 (MQ=9)                                           cAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCG.CCGGGGCGCGCGGCGAAACaaaaggccaga                                                            >  2:3105885/1‑93 (MQ=14)                                            acccGGCCCCCTTTTCTTCTTGCCCCAAATCCGCGGGGGGGCCGGGGGCG.GCC...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGgacc.gacc                                                          <  1:1702158/99‑1 (MQ=17)                                             cccGCCCCCGGTTTCTTCTGGCCCAAAAGCCGCGGGGGGCCGGGGGGCG.GGC...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGacc.gaccg                                                         <  1:344405/100‑1 (MQ=17)                                                ggCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.GCG.CGGGGCCGCGCGGCGCAACAAAAGGCC.GACCGGGc                                                      >  1:4541407/1‑101 (MQ=17)                                                 ccccccGTTTCTTCTGGCCCCAAATCCGCCGGGGGCCCGGGGGCG.GAC...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCa                                                     <  1:4205482/100‑1 (MQ=18)                                                     ccGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGGGGAAAAAAAGGCC.GGCCgggggggcc                                                 >  2:3526684/1‑95 (MQ=14)                                                        tttCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGcccccc                                              <  2:1564863/101‑1 (MQ=255)                                                         ttcttcTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCg                                             <  2:783903/101‑1 (MQ=255)                                                         ttcttcTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CGCGGGCGCGCGGGGGAACAAAAGACC.GACCGGGCAGccccccc                                             >  2:2398244/1‑100 (MQ=18)                                                         tgcttctcGGCCGAATGACGCGGGGCGCCGGGGGGGG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCg                                             <  2:4583149/99‑1 (MQ=18)                                                           cttcttGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CGCGGGCGCGCGGCGGAACAAAAGACC.CACCCGGCAGccccccccc                                           >  1:2886417/1‑98 (MQ=17)                                                            ttcttGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGGGGAAAAAAAGACC.GACCCGGCCGcccccccggc                                          >  1:3044638/1‑97 (MQ=14)                                                             tcttGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCG.CGCGGGCGCGCGGGGGAACAAAAGAAC.CAACGGGCGGCCCCCCGGGCg                                         >  2:4283433/1‑101 (MQ=14)                                                              cttGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CGCGGGCCCGCGGGGGGACAAAAGCAA.GGCCGGGCCGCCCCCCgcgccg                                        >  2:2561759/1‑96 (MQ=2)                                                               ttGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCCGCCGCGCGGCGAAACAAAAGAGC.GACCGGGCGGCCCCCCCGCCGGc                                       >  2:2919019/1‑101 (MQ=17)                                                                 ggCCCAAATCCGCCGGGGGCCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCa                                     <  2:2920751/101‑1 (MQ=255)                                                                 ggCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CGGCCGCGGCC.CGGGGGGGGAAGAAGGAGA.GACCGGGCAGCGCCCCggcgcggca                                     >  1:3039140/1‑94 (MQ=9)                                                                  gCCCAACTCCGCGGGGGGTCCGGGGGGG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAg                                    <  2:3798551/101‑1 (MQ=25)                                                                      aaacggggggggggCCGGGGGGGG.GAC...CCGGC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGaa                                <  1:4368234/92‑1 (MQ=25)                                                                      aaaTACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CCCGGCCGCGCGGCGGAACAAACGAAC.GGCCGGGCCGCCCCCCCGGCGGcgcgggac                                >  1:2210437/1‑94 (MQ=17)                                                                            gCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGGGG.CCG.CGCGGGCGCGCGGCGGAACAAAAGACCGGACCGGG.AGCCCCCCCGGCGGCCCGGGGACCCGaa                          >  1:3572567/1‑101 (MQ=12)                                                                              ggggggGCCGGGGGGGCGCC...CCCCG.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGaaa                         <  2:107879/100‑1 (MQ=37)                                                                              cGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCCCGCGGGGGAACAAAAGACC.GACCGGGCAGCCCCCCCCGCGGCCCGTGGAcccccaac                        >  1:772316/1‑96 (MQ=18)                                                                               gggggGCGGGGGGCG.GCC...CCCCG.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAAcg                       <  1:3027377/101‑1 (MQ=37)                                                                                  ggTCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCCCGCGGCGGAACAAAAGACC.GACCGGGCAGGCCCCCCGGCGGCCCGTGAACCCCAAACGCGa                    >  2:3789738/1‑101 (MQ=21)                                                                                    tCCGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGCGAAACAAAAGACC.GACCGGGCAGCCCCCCCGGCGGCCCGGGAAACCGAAACAGGAAg                  >  1:4506581/1‑101 (MQ=21)                                                                                     ccGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCC.CGCGGCCGCGCGGCGAAAAAAAAGACC.GACCCGGCAGCCCCCCCGTCGGCCAGGGAAACCGAAACGCGAAgg                 >  2:2867294/1‑101 (MQ=25)                                                                                      ggggggGG.GCC...CCCCG.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAggg                <  1:4247717/100‑1 (MQ=38)                                                                                      cGGGGGCG.GAG...CCCCC.GGCGGGGGGCCCG.CCCGGCCCCCCGCGGAACAAAAGAACC.AACCGGGCCGCCCCCCGCCCGCCCGGGCAACCCCAAAccccaaag                 >  2:3955567/1‑94 (MQ=255)                                                                                      cGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGGCGCGCGGCGGAACAAAAGACC.GACCGGGGAGCCCCCCGGTCGGCCCGGGGACCCGAAACGCGAAggg                >  2:558616/1‑101 (MQ=25)                                                                                      cGGGGGCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGGGGAACAAAGGACC.GACCGGGCAGCCCCCCCGGCGGCCCGGGGACCCCAAACCCGAAggg                >  2:2681326/1‑101 (MQ=21)                                                                                       gggggCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGGCGCGCGGCGGAACAAAGGACC.GACCGGGGAGGCCCCCCGCCGGCCAGTGAAACCGGAACGCGAAGGGa               >  2:1753231/1‑101 (MQ=25)                                                                                       gggggCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGCGGAACAAAAGACC.GACCGGGCAGCCCCCCCGGCGGCCAGTGAAACCGCAACGCGAAgggg               >  2:4305509/1‑100 (MQ=25)                                                                                        ggggCG.GAG...CCCTC.GGGGGGTCG.CCG.CGCGGCCGAGCGGCGAAACAAAGGACC.GACCGGGCAGCCGCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGAc              <  1:779281/101‑1 (MQ=255)                                                                                         gggCG.GAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGCGGAACAAAGGACC.GACCGGGCAGCCCCCCCGTCGGCCAGTGAACCCGCAAAGCGAAGGGAcg             >  2:2155437/1‑101 (MQ=37)                                                                                          ggCG.GAG...CCCCG.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGAcgc            <  2:2786150/101‑1 (MQ=255)                                                                                             g.gAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGGAACAAAGGAAC.GACCCGGCAGCCCCCCCGGCGGCCCGAGAACCCGCAAAGCGCAAGGACGCggg         >  2:1836232/1‑101 (MQ=21)                                                                                               gAG...CCCCC.GGCGGGGCG.CCG.CGCGGCCGCGCGGCGGAACAAAAGACC.GACCGGGCAGCCCCCCCGGCGGCCCGGGAAACCGCAACACGGAGGGGCGCCGGa        >  2:11152/1‑101 (MQ=19)                                                                                                 ccccccagc.ggcggGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGACGCggg         <  1:2561933/93‑1 (MQ=255)                                                                                                    cccccc.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGACGCGGGATc      <  1:3588796/100‑1 (MQ=255)                                                                                                      cccc.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGACGCGGGATCgg    <  1:1499726/101‑1 (MQ=255)                                                                                                        cc.GGCGGGTCG.CCG.CGCGGCCGCGCCGCGGAACAAAAGACC.GACCCGGCAGCCCCCCCGCCCGCCACGGAACCCGAAACCCGAAGGGACGGGGGGGCgggg  >  2:2553004/1‑101 (MQ=255)                                                                                                         |                                                                                                        CACGACGGGGGCAAGGGGCAATGCGGCGCAAGGCCCCCCGGGCAACCGGCCCCCGTTTCTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCG.GAG...CCCCC.GGCGGGTCG.CCG.CGCGGCCGCGCGGCGAAACAAAGGACC.GACCGGGCAGCCCCCCGGTCGGCCAGTGAACCCGAAACGCGAAGGGACGCGGGATCGGGG  >  NC_014034/3276288‑3276487 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG