New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330295	29 (0.120)	53 (0.230)	18/192	18.3	0.65	intergenic (+270/+42)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	2330296 =	29 (0.120)					intergenic (+271/+41)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

AGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTG  >  NC_014034/2330206‑2330396                                                                                                 |                                                                                                            aGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G....cggagcccccg                                                                                              <  2:4839135/101‑11 (MQ=38) aGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGT.CCGGG..G....G....cggagcccccg                                                                                              <  1:3618665/101‑11 (MQ=38)        gCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTc                                                                                            <  2:3977837/101‑1 (MQ=25)        gCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTc                                                                                            <  2:4527515/101‑1 (MQ=25)           ggggCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAGCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGcc                                                                                         >  1:3519875/1‑101 (MQ=25)            gggCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCg                                                                                        >  1:3734938/1‑101 (MQ=25)                gcgcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.c                                                                                   <  1:4047848/101‑1 (MQ=25)                  gcATGCGGGGCCCCGGATCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CAt                                                                                 <  2:2842084/101‑1 (MQ=21)                  gcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGccccgggga                                                                                  >  2:4490551/1‑94 (MQ=18)                  gcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGCgggcc                                                                                  >  1:1916078/1‑98 (MQ=21)                   cATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGCCGGGG.Cagc                                                                                >  2:2963620/1‑99 (MQ=21)                      gCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGcc                                                                             <  2:4189205/101‑1 (MQ=25)                      gCGGGCCCCCGGATCCCCGGCGGCCCGGGCGGCTTCCACCTGGGCCCAAAGACCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGcc                                                                             <  2:1126476/101‑1 (MQ=17)                       gggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCt                                                                            <  2:1949216/100‑1 (MQ=21)                       cGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCt                                                                            <  2:4871098/101‑1 (MQ=25)                        ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTc                                                                           <  2:3760319/101‑1 (MQ=25)                            ccccGGATCCCCGGCGGCCCGGGCGTCTCTCCCGGGGGGCAAAAGCCCCGGGGGGTCGGGGGGCG....GCC..CCCCCGGCGGGTCTCCGAGG.CATCGCCTCGGCg                                                                       <  2:4648946/101‑1 (MQ=255)                              ccGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGaa                                                                     <  2:2423393/101‑1 (MQ=25)                               cGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCCGGG.CCTCGCCCCCGCGgaa                                                                    >  1:208004/1‑101 (MQ=12)                                  aTCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCCGGG.GAGCGCCCCGGGGaaaaac                                                                 >  1:2965108/1‑98 (MQ=9)                                   tCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGAGTCGCCGAGG.CATCGCCTCGGCGAAATccc                                                                <  1:4493882/101‑1 (MQ=25)                                   tCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGCCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATccc                                                                <  2:3129602/101‑1 (MQ=21)                                   ccccgggcggcCGGGGCGGCTTTCCCCGGGGCCAAAAGACCCGGGGGGCCGGGGG..G....GGGGCCCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATccc                                                                <  1:2606103/96‑1 (MQ=12)                                     gcgggcggcCCGGGCGTGTTTCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCtt                                                              <  2:175083/98‑1 (MQ=18)                                     cccGGCGGCCGGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCtt                                                              <  2:4152876/100‑1 (MQ=21)                                     aCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGACCCCGGGGGGCCGGGG..GCGGAG....CCACCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCtt                                                              <  1:3310859/101‑1 (MQ=255)                                       cggcggCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAg                                                            <  2:564892/101‑1 (MQ=25)                                        ggcggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGCCGCCGCGGCCACCCCCCGGGCGAAACCCCttgt                                                            >  2:3903631/1‑99 (MQ=9)                                          cggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTaa                                                         <  2:740959/101‑1 (MQ=25)                                            gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAg                                                       <  1:4739205/101‑1 (MQ=21)                                            gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGGGG.CAGCGCCCCGGCGGAATCCCCTAGTaaaa                                                       >  2:466379/1‑100 (MQ=12)                                             ccggggCGGCTTTCACCGGGGCCCAAAGACCCCGGGGGTCGGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.a                                                     <  2:3215778/98‑1 (MQ=18)                                               cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.Acc                                                   <  1:4636947/101‑1 (MQ=25)                                                gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGCCGAGG.CGTCGCCTCGGCGGAAACCCCTAGTAAAA.Accc                                                  >  1:2168820/1‑100 (MQ=12)                                                   cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.Accgccc                                               <  2:446753/101‑1 (MQ=25)                                                   cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGGGG.CATCGCCTCCGCCAAAAACCCTAGTaaaaaaccccc                                                >  1:3392046/1‑93 (MQ=9)                                                     gcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGCGG.CAACGCCCCCGCGGAAACCCCTAGTAAAA.Accgcccgc                                             >  1:3910916/1‑101 (MQ=9)                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGCCGGGG.GCGCGCTTCGGCGGAATTCCCTAGTAACG.aacctccgccg                                           >  2:4889942/1‑91 (MQ=2)                                                       tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGGGG.CCACGCCCCCGCGAAAACCCTTATTAAAA.Acaaaccccgg                                           >  2:4216937/1‑92 (MQ=2)                                                         tCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGCCGAGG.CGTCGCCTCGGCGGAAACCCCTAGTAAAGAACCCCCcgcgac                                          >  2:1178479/1‑99 (MQ=9)                                                         cgaCCTGGGCCGAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.c                                        <  2:1501919/99‑1 (MQ=18)                                                          cACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCCGGG.GATCGCCCCCGCGGAAACCCCTTGTAAAA.Aacgcccgccggca                                        >  2:3665165/1‑96 (MQ=2)                                                             cTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAggg                                    <  2:2198929/101‑1 (MQ=21)                                                             cTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGCGG.GATCGCCTCCGCCGAAACCCCTCGTAAAA.Aacgccccccgggcagg                                     >  1:1913742/1‑91 (MQ=0)                                                               ggggCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGCCGGGG.CCTCGCCCCGGCGAAAACCCCTAGTAAAA.ACCGACCCCGGG.CACGGaa                                  >  2:420162/1‑100 (MQ=2)                                                                gggCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGGGGCCGGG.CATCGCCCCGGGGGAAACCCTTCGTTAAG.AACGCCCCCGGG.CAGGGGTc                                 >  1:2476392/1‑101 (MQ=2)                                                                 ggCCAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATcc                                <  2:4305162/101‑1 (MQ=21)                                                                  gCCAAAGACCCCGGGGGTCGGGGG..GCGGAG....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCg                               <  1:1618085/101‑1 (MQ=21)                                                                    cAAAGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGGGG.GATCGCCTCGGCGGAAACCCTTTTTTAAA.ACCGCCCCCGGG.CAGGGAGCCGaa                             >  1:4519947/1‑101 (MQ=2)                                                                      aaGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGCGG.CATCGCCTCCGCGAAATCCCTTAGTAAAA.AACGCCCCCGGACCAGGGA.CCGAAgg                           >  2:2982340/1‑101 (MQ=9)                                                                       aGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCGAGG.CATCGCCCCGGCGGAAACCCTTAGTAAAA.ACCGCCCGCGGG.CAAGGGTCCGAAggc                          >  2:397724/1‑100 (MQ=12)                                                                       aGATCCCGGGGGTCCGGGG..GCGGAG....CCCCCGGCGGGGCGCCCAGG.CCCCGCCCCCGCGAAAACCCCTAGTAAAA.ACCCCCCGCGGG.CAGGGAACCGAAggg                          >  1:3241033/1‑100 (MQ=2)                                                                                   gggccgg..g....g....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATc          <  2:2894652/96‑1 (MQ=255)                                                                                       cgggggcggag....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGa            <  1:4970217/91‑1 (MQ=255)                                                                                        gggggcggag....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGAt           <  2:2964880/92‑1 (MQ=255)                                                                                        gg..g....g....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCg     <  1:200422/101‑1 (MQ=255)                                                                                            gcggag....CCCCCGGCGGGTCGCCGAGG.CATCGCCCCGGCGAAAACCCCTAATAAAA.ACCGCCCCCGGA.CAGGGATCCGAAGGGCGCCTTCTTCGGGGTCAcc       >  2:4545248/6‑101 (MQ=25)                                                                                             cggag....CCCCCGGCGGGTCCCCGAGG.GACCTCCTCGGGGAAATCCCTTAGTAAAG.ACCGCCCGCCGA.CAGGGATCCGAAGGGCGCCTTTTTCGGGATAAccc      >  2:883066/5‑101 (MQ=255)                                                                                             cggag....CCCCCGGCGGGGCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGGCGCCTTCTTCGGGGTCAccc      >  2:2994880/5‑101 (MQ=39)                                                                                              ggag....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCg     <  1:4553362/98‑1 (MQ=255)                                                                                              ggag....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCCTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCg     >  2:2604041/4‑101 (MQ=255)                                                                                              ggag....CCCCCGGCGGGGCGCCGAGG.CATCGCCCCGGCGAAAACCCTTAGTAAAG.ACCGCCCGCGGG.CAGGGATCCGAAGGGCGCCTTCTTCGGGATCACCCg     >  2:4919707/4‑101 (MQ=255)                                                                                               gag....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAA.AACGCCCGCGGG.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCAccccc    >  2:3319072/3‑99 (MQ=38)                                                                                                 g....CCCCCGGCGGGTCGCCGAGG.CATCGCCCCGGCGAAATCCCTTAGTAAAA.ACCGCCCGCGGA.CAGGGGTCCGAAGGGCGCCTTCTTCGGGGTCAcccccct  >  2:728872/1‑97 (MQ=38)                                                                                                 |                                                                                                            AGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G....CCCCCGGCGGGTCGCCGAGG.CATCGCCTCGGCGAAATCCCTTAGTAAAG.ACCGCCCGCGGA.CAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTG  >  NC_014034/2330206‑2330396 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG