New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330290	31 (0.160)	33 (0.170)	24/180	16.2	0.38	intergenic (+265/+47)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	3276374 =	75 (0.350)					intergenic (‑126/+123)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

CGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330190‑2330373                                                                                                     |                                                                                                  cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  2:3996946/101‑1 (MQ=255) cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  1:62403/101‑1 (MQ=255)  ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                                  <  1:3684590/101‑2 (MQ=255)   gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGatcccggggg.cccgg                                                                                                >  1:859780/1‑101 (MQ=255)   gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  1:1644508/101‑3 (MQ=255)   gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  2:2412673/101‑3 (MQ=255)    cGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggg                                                                                                >  2:75346/1‑101 (MQ=255)     gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:496104/1‑101 (MQ=255)     gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:2263649/1‑101 (MQ=255)     gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               <  1:3052015/101‑1 (MQ=255)      tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            <  1:714198/101‑1 (MQ=255)      tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            >  1:1901/1‑101 (MQ=255)        tttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcg                                                                                          >  1:374631/1‑99 (MQ=255)          tGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcgga                                                                                        <  2:2991344/101‑5 (MQ=255)             gcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcc                                                                                     <  1:2551832/101‑8 (MQ=255)             gcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcc                                                                                     <  2:122333/101‑8 (MQ=255)               cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcccc                                                                                   >  2:957855/1‑92 (MQ=38)               cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagcccc                                                                                   >  1:1322437/1‑92 (MQ=38)               cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G.....cggagcccc                                                                         <  1:75361/101‑9 (MQ=38)                aaGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..gcggagccccc                                                                                  >  1:815853/1‑91 (MQ=38)                 aGAAAACGCCGGGGCGCGCGTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGTCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G.....cggagcccccg                                                                       <  1:1102860/101‑11 (MQ=25)                         ccGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCg                                                                   <  1:1947808/101‑1 (MQ=25)                           ggggCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGcc                                                                 >  1:2556730/1‑101 (MQ=25)                              gcgggcATGCGGGGCCCCGGAGCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAg                                                              <  1:633093/101‑1 (MQ=18)                              gcgcgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAg                                                              <  2:1812091/101‑1 (MQ=25)                                gcgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGc                                                            <  2:2760031/101‑1 (MQ=25)                                 cgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGCGGcc                                                           >  2:257504/1‑100 (MQ=21)                                   cATGCGGGGCCCGGGATCCCCGGCGGCCGGGGCGGCTTTCACCGGGGGCAAAAGATCCCGGGGGTCCGGGG..GGGGAG.....CCCCCGGC.GGGTCGCCGAGGCATc                                                         <  2:2188654/101‑1 (MQ=18)                                    aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTGGcccgggcgggc                                                        >  1:358864/1‑92 (MQ=18)                                    aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGGGCCGCGGGATCg                                                        >  1:1809229/1‑101 (MQ=21)                                      gCGGGGCCCCGGATCCCCGGCGGCCGGGGCGGCTTTCACCGGGGGCCAAAGACCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGcc                                                      <  2:2556539/101‑1 (MQ=18)                                        ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTc                                                    <  2:261005/101‑1 (MQ=25)                                        ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGGGCCGCGGCGTCGcccc                                                    >  1:617489/1‑99 (MQ=18)                                            ccccGGATCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.g                                              <  2:3004245/101‑1 (MQ=21)                                                ggATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAAt                                          <  2:3473194/101‑1 (MQ=25)                                                    cACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGGGCGCCTCG.GC.GAGAAcccc                                      >  2:3928336/1‑100 (MQ=12)                                                     ccgggcggcCGGGGCGTCTTCCCCGGGGGGCAAAAGCCCCGGGGGGTCCGGGGGCG....GCC...CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCtt                                     <  2:1809110/98‑1 (MQ=9)                                                     ccgggcggcCGGGGCGGTTTCCACCGGGGGCAAAAGACCCGGGGGGCCGGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCtt                                     <  1:1485843/98‑1 (MQ=12)                                                       cggcggCCCGGGCGGTTTCCCCCGGGGGCCAAAGA.CCCGGGGGGCCCGGG..G....GCGGGCCCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAg                                   <  1:3568247/101‑1 (MQ=16)                                                        ggcggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCCGGGCAGCGCCGCC.GCGGAAAACCCtttg                                   >  2:1297074/1‑99 (MQ=9)                                                          cggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCGGCGCCCCGCCC.GAAACCCCttctaa                                 >  1:4125875/1‑97 (MQ=9)                                                           ggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGAGGGACCGCCCCT.GC.GCAAACCCCTTGTaaa                               >  2:3225069/1‑101 (MQ=9)                                                           ggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCCCGGCCGCCCCCCG.GC.CGAAACCCCTAGTaaa                               >  1:3929461/1‑101 (MQ=2)                                                              ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGACGGATCCCCCCG.GCGGAAAACCCtacgaaaaca                             >  2:4217125/1‑92 (MQ=9)                                                               cGGGCGGCTTTCCCCGGGGCCCAAAGTCCCGGGGGGTCCGGGG..GGGGCG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAcc                           <  2:374580/101‑1 (MQ=16)                                                               cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAcc                           <  2:3459546/101‑1 (MQ=25)                                                                gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGCGGCAACGCCCCG.GG.GAAAACCCCTatgaaaaacac                          >  2:3891299/1‑91 (MQ=9)                                                                  gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGGTCGCCCCC.GC.GGCAACCCTTTGTAAAAAccgcc                        >  1:1889128/1‑101 (MQ=9)                                                                    ggcTTCCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAccgcccg                      <  2:3780415/101‑1 (MQ=21)                                                                     gcTTTCACCGGGGGCCAAAGACCCCGGGGGTCGGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGAccgcccgc                     <  2:3005977/101‑1 (MQ=21)                                                                      cTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGATCGCCCCC.GCGGAAAACCCTT.GTAAAAACCCCCcccg                    >  1:1474315/1‑101 (MQ=2)                                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGGCGAGGGGTCGCCCCC.GC.GGAATCCCCCATTAAAAAACGCCCCCgg                   >  1:792814/1‑101 (MQ=2)                                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGGATCGCCCCG.GC.GAAAACCCCTAGTAAAAAacgccccccg                   >  1:2307711/1‑97 (MQ=9)                                                                         tCACCTGGGGCCAAAGAGCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGAc                 <  2:2454810/101‑1 (MQ=21)                                                                             cTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCCCCGCCTCC.GC.GAAATCCCCTTTTAAAAAACCCCCGCCGCCAggg             >  1:1403811/1‑101 (MQ=0)                                                                              tGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGGCGCC.AGGCCGCGCCCCC.GC.GCAAACCCTTCCTTAAAAACGCCCCCGGGCAGGGa            >  1:557496/1‑101 (MQ=2)                                                                                   ccAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGa       <  2:1522890/101‑1 (MQ=21)                                                                                        gATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGC.GGGGCGCCGGGGCATCGCCTCG.GC.GAAAACCCTTAGTAAAAACCGCCCGCGGGCAGGGGGCCGAAgggc  >  2:183346/1‑99 (MQ=12)                                                                                                     |                                                                                                  CGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330190‑2330373 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG