New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1103383	91 (0.480)	32 (0.170)	17/180	19.6	0.34	intergenic (‑383/+35)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	= 2330280	32 (0.150)					intergenic (+255/+57)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330180‑2330373                                                                                                     |                                                                                                            cccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtc                                                                                                             <  1:924742/101‑1 (MQ=255)  ccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcc                                                                                                            <  1:3908986/101‑1 (MQ=255)   cGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtccc                                                                                                           >  2:205535/1‑101 (MQ=255)     cACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgg                                                                                                         >  2:714122/1‑101 (MQ=255)      aCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccggg                                                                                                        >  1:3997206/1‑101 (MQ=255)      aCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccggg                                                                                                        >  2:3403283/1‑101 (MQ=255)         cccGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggt                                                                                                     <  2:118395/101‑1 (MQ=255)           cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  1:62403/101‑1 (MQ=255)           cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                                   <  2:3996946/101‑1 (MQ=255)            ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                                  <  1:3684590/101‑2 (MQ=255)             gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGatcccggggg.cccgg                                                                                                >  1:859780/1‑101 (MQ=255)             gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  2:2412673/101‑3 (MQ=255)             gCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgg                                                                                                 <  1:1644508/101‑3 (MQ=255)              cGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggg                                                                                                >  2:75346/1‑101 (MQ=255)               gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:2263649/1‑101 (MQ=255)               gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               <  1:3052015/101‑1 (MQ=255)               gTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg                                                                                               >  2:496104/1‑101 (MQ=255)                tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            >  1:1901/1‑101 (MQ=255)                tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggg..g                                                                                            <  1:714198/101‑1 (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)                                                                                                     |                                                                                                            CCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGC.GGGTCGCCGAGGCATCGCCTCG.GC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330180‑2330373 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG