New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392474	45 (0.230)	14 (0.070)	11/166	22.0	0.21	intergenic (‑122/+21)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	2330313 =	60 (0.250)					intergenic (+288/+24)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....G.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCGA  >  NC_014034/2330222‑2330408                                                                                                       |                                                                                                  cgcgggCGGGCCCCCGG.ATCCCGGGCGGCCCGGGC.GCCTTCCCCCGGGGCCAAAAGACCCGGGGGGCCGGGGG....GCGGCCCCCCC.GGCGGGTCGCCGAGGCa                                                                                              <  2:3484496/96‑1 (MQ=9)    aTGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCg                                                                                           <  2:767480/101‑1 (MQ=25)     gggcgggCCCCGGCACCCCCGGCGGCCCGGGCGGTTTCCCCCGGGGGCAAAAGACCCGGGGGGCCGGGGGG....GGGA..CCCCCGGGCGGGTCGCCGAGGCATCg                                                                                           <  2:472147/97‑1 (MQ=255)        ggggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTc                                                                                       <  1:1852478/101‑1 (MQ=25)        ggggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGCGTccgctc                                                                                       >  2:3883360/1‑96 (MQ=18)          ggCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGGGGCGGCGGCTC.gg                                                                                    >  2:4418041/1‑101 (MQ=16)                 g.ATCCCCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATc                                                                            <  2:1569853/101‑1 (MQ=21)                     cccggggggcCGGGGCGGTTTCCACCGGGGGCAAAAGATCCGGGGGGTCGGGGGG....GGGGC.CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATccgt                                                                         <  1:4002500/94‑3 (MQ=12)                      cccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCtt                                                                        <  1:1128621/100‑1 (MQ=21)                       ccGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGACCGCCCC.CGCGGAAACCCCtt                                                                        >  2:1305341/1‑101 (MQ=9)                        cggcggCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAg                                                                      <  1:3565725/101‑1 (MQ=25)                         ggcggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGt                                                                     <  1:4327313/101‑1 (MQ=25)                           cggcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGATCGCCCC.GGC.GAAAACCCCTTGTaa                                                                   >  1:2896382/1‑101 (MQ=12)                            ggcCGGGGCGGCTTTCACCTGGGGCCAAAGACCCGGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTaaa                                                                  <  2:1204711/101‑1 (MQ=21)                            ggcCCGGGCGGCTTTCCCCGGGGGCCAAAGATCCCGGGGGTCGGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTaaa                                                                  <  2:3384193/101‑1 (MQ=21)                             gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAg                                                                 <  1:3967738/101‑1 (MQ=25)                             gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGCCCCCCTC.CGC.GAACACCCTTCGTaaaa                                                                 >  2:2540011/1‑100 (MQ=9)                              ccggggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGa                                                                <  2:224891/98‑1 (MQ=21)                              ccggggCGGC.TTCCCCCGGGGGCAAAGGACCCGGGGGGCCGGGGG....GCGGA.CCCCCGGGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGa                                                                <  1:2911336/98‑1 (MQ=255)                               ccGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGAACGCCCC.CGCGGAAAACCCtcgtcaaaac                                                                >  1:3262484/1‑92 (MQ=2)                                cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGATCGCCCC.GGCGGAAAACCCtcttcaaaaac                                                               >  2:3401721/1‑91 (MQ=9)                                cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGCGTCGCCCCGGGG.GAAACCCCTTGTTAAAAAc                                                               >  1:3856951/1‑101 (MQ=9)                                 gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGCGGCATCGGCTC.GCC.GGACGCCCCTAATAAACAccg                                                             >  1:493771/1‑101 (MQ=9)                                  ggcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgc                                                            <  2:4730808/101‑1 (MQ=25)                                  ggcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgc                                                            <  1:3557513/101‑1 (MQ=25)                                   gcggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgcc                                                           <  2:2817226/101‑1 (MQ=25)                                    cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGAccgccc                                                          <  2:3193896/101‑1 (MQ=25)                                     ggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGATCGCCCC.CGC.GGAAACCCTTTGTAAAAAacgcccc                                                         >  1:784390/1‑100 (MQ=9)                                      gcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGGGCCGAGGGATCGCCCC.CGC.GAAAACCCTTAGTAAAAAacgccccc                                                        >  1:4642127/1‑99 (MQ=12)                                      gcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCCC.GGC.GAAATCCCTTTGTAAAGAccgcccgc                                                        >  1:2296432/1‑101 (MQ=21)                                        tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCCCCTC.CGC.GTAAAACCTTACTAAAAAACACCCCCgg                                                      >  1:2909700/1‑101 (MQ=9)                                         ttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCCGGGGATCGCCCC.CGC.GAAAAACCCTAGTAAAAAacgccccccgg                                                     >  1:3726270/1‑96 (MQ=2)                                          tCACCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGCCCGCCCGCGGAc                                                    <  1:2561865/101‑1 (MQ=21)                                          ccccgtGGGGCAAAAGACCCCGGGGGCCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGAc                                                    <  2:2763526/96‑1 (MQ=18)                                            aCCGGGGGCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAg                                                  <  2:4450498/101‑1 (MQ=21)                                                 gggCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGGCCAGGCCGCGCCCC.CTC.GGAAATCCTTAGTAAAAAACCCCCGCCGACAGGGGTc                                             >  1:1537311/1‑101 (MQ=2)                                                  ggCCAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATcc                                            <  2:3021403/101‑1 (MQ=21)                                                    ccAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCCC.CGC.GAAAACCCCTAGTAAAAACCGCCCGCGGACAAGGAGCCGa                                          >  2:3109316/1‑101 (MQ=12)                                                     cAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGGGGGCTCGCCCC.CGG.GGAAACCCCTAGTAAAGAACGCCCCCGGGCAGGGGTCCGaa                                         >  1:2729159/1‑101 (MQ=0)                                                     cAAAGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCGGGATCGCCCC.GGC.GAAAACCCTTAGTAAAAAACGCCCGCGGGCAGGGATCCgga                                         >  2:4675243/1‑99 (MQ=9)                                                     cAAAGACCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGaa                                         <  1:4262192/101‑1 (MQ=21)                                                      aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAg                                        <  1:1548351/101‑1 (MQ=21)                                                      aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGCAGAATCGCCTC.GGC.GCAAAGCCCTCTTTATTACCGCCCCCGGACAGGGAGGCGAAg                                        >  2:2596258/1‑101 (MQ=0)                                                      aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGCTCGCCTC.CGC.GCAAACCCCTTCTAAAAACCCCCCCCGGGGAggggaccgcag                                        >  1:1864919/1‑93 (MQ=0)                                                      aaaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGCATCGCCTC.GGC.GAAAACCCTTAGTAAAAAACGCCCGCGGGCAGGGATCCGAAg                                        >  1:2147643/1‑101 (MQ=18)                                                       aaGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGGCGGGGGGTCGCCCC.CGCGGAAACCCCTTA.TAAAAACCGCCCGCGGGCAGGGAGCCGGAgg                                       >  1:1042408/1‑101 (MQ=0)                                                        aGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGt                                      <  2:540983/101‑1 (MQ=25)                                                        aGATCCCGGGGGTCCGGGGGCGGAG.....CCCCC.GGCGGGGCGCCGAGGGATCGCCTC.GGC.GAAATCCCCTAGTAAAAACCCCCCGCGGGCCAGGATCCGCAggg                                      >  2:2844906/1‑100 (MQ=9)                                                                       gggggtggag.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGAt                       <  1:2170131/92‑1 (MQ=255)                                                                       gcggg....c.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAcc                   <  2:3782478/99‑1 (MQ=255)                                                                        ggggcggag.....CCCCC.GGCGGGTCGCCGGGGCATCGCCCC.GGC.GAAAACCCTTAGTAAAGACCGCCCCCGGAGAGGGATCCCCAGGACGCCCTTTTCGGGGTc                      >  2:3466531/9‑101 (MQ=16)                                                                           gcggag.....CCCCC.GGCGGGTCGCCCAGCCATCGCCCC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGGCACGGATCCGAAGGTCGCCTTCTTCGGGATCAcc                   >  2:3773245/6‑101 (MQ=255)                                                                           g....g.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCt               <  2:2074198/101‑1 (MQ=255)                                                                            cggag.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAccc                  <  2:785142/97‑1 (MQ=255)                                                                             ggggcggccccccc.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATc                      <  1:1948011/92‑1 (MQ=255)                                                                                gcggacccccc.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAcc                   <  2:309089/95‑1 (MQ=255)                                                                                g.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTg              <  2:493720/101‑1 (MQ=255)                                                                                 gggccccccc.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAccc                  <  1:3525539/96‑1 (MQ=255)                                                                                      ccccc.GGCGGGTCGCCGAGGCATCGCCCC.GGC.GCAATCCCTTTGTAAAAACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCNTCGGGGTCAccccccgt             >  2:483496/1‑96 (MQ=255)                                                                                       cccc.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGtt            <  1:3674270/101‑1 (MQ=255)                                                                                         cc.GGCGGGGCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAAACCGCCCGCGGACAGGGATCCGAAGGGCGCCTTCTTCCGGATCACCCCCTGTTcc          >  2:1108113/1‑101 (MQ=255)                                                                                          ggggcggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTcc          <  1:2596410/99‑1 (MQ=255)                                                                                            ggcggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTcccc        <  1:1677424/101‑1 (MQ=255)                                                                                            ggcggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTcccc        <  2:2846704/101‑1 (MQ=255)                                                                                            ggcggGTCGCCGAGGCATCCCCCC.CGC.GAAAACCCCTAGTAAAAACCGCCCGCGGACAGGGATCCCAAGGGCGCCCTCTTTCGGATCACCCCCTGTTcccc        >  2:1463104/1‑101 (MQ=255)                                                                                              cggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCgg      >  2:3052595/1‑101 (MQ=255)                                                                                              cggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCgg      >  1:2074870/1‑101 (MQ=255)                                                                                              cggGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCgg      >  1:2924377/1‑101 (MQ=255)                                                                                               gggTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt     >  2:3790418/1‑101 (MQ=255)                                                                                               gggTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt     >  2:762311/1‑101 (MQ=255)                                                                                               gggTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt     <  2:784317/101‑1 (MQ=255)                                                                                                ggTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTc    >  1:299550/1‑101 (MQ=255)                                                                                                 gTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCg   <  2:3568546/101‑1 (MQ=255)                                                                                                  tCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCGa  >  1:1064128/1‑101 (MQ=255)                                                                                                       |                                                                                                  CGCATGCGGGGCCCCGG.ATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGGG....G.....CCCCC.GGCGGGTCGCCGAGGCATCGCCTC.GGC.GAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCGA  >  NC_014034/2330222‑2330408 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG