New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330290	28 (0.140)	22 (0.110)	17/180	22.1	0.32	intergenic (+265/+47)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	3276374 =	64 (0.280)					intergenic (‑126/+123)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

CGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....GCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330190‑2330373                                                                                                     |                                                                                        cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAATAtcccgggggtcc                                                                                         >  1:2937736/1‑101 (MQ=255) cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                         <  2:1428217/101‑1 (MQ=255) cGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtcc                                                                                         <  1:149659/101‑1 (MQ=255)  ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                        >  1:4288523/1‑100 (MQ=255)  ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                        <  1:3591641/101‑2 (MQ=255)  ggCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccg                                                                                        >  1:3251242/1‑100 (MQ=255)    cGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggg                                                                                      <  1:111410/101‑1 (MQ=255)      tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccggggg                                                                                    <  1:961024/101‑1 (MQ=255)      tATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCAACTGGGGCCAAAGAtaccgggggtccggggg                                                                                    >  2:1762967/1‑101 (MQ=255)       aTTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggc                                                                                   >  2:2498458/1‑100 (MQ=255)        tttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcg                                                                                  >  1:1218570/1‑99 (MQ=255)         ttGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcgg                                                                                 <  2:495437/101‑4 (MQ=255)          tGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcgga                                                                                <  2:3828694/101‑5 (MQ=255)           gcgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggag                                                                               <  1:2498621/101‑6 (MQ=255)           gcgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggag                                                                               <  2:4159660/101‑6 (MQ=255)           gcgcCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggag                                                                               <  1:4234172/101‑6 (MQ=255)               cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGGCCAAGAtcccgggggtccgggggcggagcccc                                                                           >  2:64940/1‑92 (MQ=38)               cAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGGG....Gcggagcccc                                                                      <  1:3998271/101‑9 (MQ=38)                aaGAAAAGGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagccccc                                                                          >  1:282233/1‑91 (MQ=37)                aaGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAtcccgggggtccgggggcggagccccc                                                                          <  2:1780537/101‑11 (MQ=38)                aaGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGGG....Gcggagccccc                                                                     <  2:903932/101‑10 (MQ=38)                                  gcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGccccgggcc                                                        >  1:2942257/1‑94 (MQ=18)                                    aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGGCGAgggggcg                                                      >  2:3969899/1‑96 (MQ=21)                                         gggCCCCAGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGCATCGccccc                                                 >  2:2137666/1‑98 (MQ=21)                                                 gATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGGGCCGAGGGATCGCCCCGGCGaaaac                                         >  2:2640028/1‑99 (MQ=18)                                                    cACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGGGGCGTGGCCCCCGCGCAAACCCt                                      >  2:2202601/1‑101 (MQ=12)                                                     cccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCtt                                     <  2:191303/100‑1 (MQ=21)                                                      ccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAGCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTa                                    <  2:2243913/101‑1 (MQ=25)                                                              ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAc                            <  2:689728/101‑1 (MQ=25)                                                              ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAc                            <  2:2743233/101‑1 (MQ=25)                                                              ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGGGCCGGGGCCTCGCCCCCGCGAAAACCCCTAGTAAACAc                            >  2:3241828/1‑101 (MQ=12)                                                                gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccg                          <  1:1435186/101‑1 (MQ=25)                                                                  gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGCGGGGGCGCCTCCGCGGAAACCCCTTGTAAAGaacccc                        >  1:3392350/1‑96 (MQ=2)                                                                  gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGCAGCGCCCCGGCGAAATCCCCTAGTAAAAAacgcc                        >  1:4179500/1‑101 (MQ=16)                                                                   cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCTCCTCGGCGAAATCCCTTAGTAAAGAccgccc                       <  1:3960877/101‑1 (MQ=21)                                                                    ggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGGGCCCGGGCATCGCCCCCGCGAAAAACCCTCGTAAAAAacgcccc                      >  1:3042813/1‑100 (MQ=2)                                                                      cTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGGGGCATCGCCTCGGCGAAAACCCCTTGTAAAAACCGCCcccg                    >  2:4078441/1‑101 (MQ=12)                                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGGCCCGGCGCCCCCTCGGCCGAATCCCCTAATGAAAAacgcccgccc                   >  2:3883915/1‑99 (MQ=2)                                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGCATCGCCTCCGCGAAAAACCTCTGTAAAAAAAGCCCGCgg                   >  2:3823067/1‑101 (MQ=9)                                                                         tccccgggggCCAGAGATCCCGGGGGGCGGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGAc                 <  2:2942036/95‑1 (MQ=18)                                                                          cACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGGGGAGCCCCGGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACa                <  2:3254669/101‑1 (MQ=25)                                                                          cACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGGGGGATCGCCTCGGCGAAAACCCTTTGTTAAAACCGCCCGCGGACa                >  2:3000139/1‑101 (MQ=12)                                                                               ggggCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGGATCGCCCCCGCGGAAAACCTTAGTAAAGAACGCCCGCGGACAgggga           >  1:2308054/1‑99 (MQ=9)                                                                                    cAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCCTCGCCCCGGCGAAAAACCCTAGGAAAAAACGCCCGCCGGCACGGCTCCgca      >  2:1757986/1‑99 (MQ=2)                                                                                    cAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGGATCGCCCCGGCGAAAACCCTTAGTAAAGACCGCCCGCGGGCAgggggcccca      >  2:3484652/1‑94 (MQ=12)                                                                                     aaaGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAg     <  1:1485819/101‑1 (MQ=21)                                                                                      aaGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGGGGGATCGCCCCCGCGGAAAACCCTAGTAAAAAACGCCCCCGGGCAAGGGGCCGCAgg    >  1:3456122/1‑101 (MQ=0)                                                                                      aaGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGGGTCGCCCCGGCGAAATACCCTTGTAAAAACCGCCCGCGGACAGGGGACCGAAgg    >  2:86705/1‑101 (MQ=9)                                                                                       aGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGTGCCGAGGCCTCGCCTCCGCGAAAACCCCTCGTAAAGAACCCCCCCGGGCAGGGAGCCGaaagg   >  1:2033442/1‑98 (MQ=2)                                                                                        gATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGGCGCCGAGGGATCGCCCCGGCGAAAACCCCTAGTAAAAAACCCCCCCGGACAGGGATCCGAAgggc  >  1:662947/1‑99 (MQ=9)                                                                                                     |                                                                                        CGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....GCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTC  >  NC_014034/2330190‑2330373 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG