New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 504736 =209 (0.890)43 (0.180) 5/192 26.2 0.25 intergenic (+9/+101) trpS/RCAP_rcc00470 tryptophanyl‑tRNA synthetase/MATE efflux family protein
?NC_014034 = 2330171 46 (0.190)intergenic (+146/+166) RCAP_rcc02161/mrcA hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

TTTTCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......CGG.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCG  >  NC_014034/2330071‑2330245
                                                                                                    |                                                                                            
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              <  2:4796559/101‑1 (MQ=255)
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              <  1:46858/101‑1 (MQ=255)
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              >  2:4691597/1‑101 (MQ=255)
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              >  1:4705895/1‑101 (MQ=255)
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              <  1:2321436/101‑1 (MQ=255)
ttttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCg                                                                                              <  2:2810410/101‑1 (MQ=255)
  ttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGAGCCcgg                                                                                            >  1:1949353/1‑101 (MQ=255)
  ttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCggg                                                                                            >  1:3496424/1‑101 (MQ=255)
  ttCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCggg                                                                                            <  2:4418048/101‑1 (MQ=255)
   tCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGgc                                                                                           <  2:4454501/101‑1 (MQ=255)
     ggCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGGCCCcggggg                                                                                         >  1:1126590/1‑98 (MQ=255)
      gCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCggggggg                                                                                        >  2:4251068/1‑97 (MQ=255)
       cTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggg                                                                            >  1:4684641/1‑101 (MQ=255)
        ttGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Gggg                                                                           >  2:4047545/1‑100 (MQ=255)
        ttGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Gggg                                                                           >  1:4153193/1‑100 (MQ=255)
         tGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggg                                                                          >  1:1180639/1‑99 (MQ=255)
         tGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggc                                                                          <  1:21854/101‑3 (MQ=255)
         tGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggc                                                                          >  1:564971/1‑99 (MQ=255)
          ggCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCggggcgggggg                                                                                    >  2:1833358/1‑93 (MQ=255)
            ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGGTCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggctcc                                                                       <  1:771653/101‑6 (MQ=255)
            ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggctcc                                                                       <  1:1201483/101‑6 (MQ=255)
            ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggctcc                                                                       <  1:4081553/101‑6 (MQ=255)
            ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggctcc                                                                       <  2:3711830/101‑6 (MQ=255)
            ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......Ggggctcc                                                                       <  2:572004/101‑6 (MQ=255)
               ccGCCAAGGGGGCCAACGGCGCGCAGAGCGCCGCGCGGATCGGCCGATGGCGGAGAGGAATTTCGCCTCGCAGGCGCGGCGACCGGGGC....G.......Ggggctccgcc                                                                    <  2:4550536/101‑9 (MQ=37)
                                       agagCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTgcgc                                            <  1:480302/101‑1 (MQ=18)
                                         agCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCa                                          <  1:3967207/101‑1 (MQ=18)
                                         agCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCa                                          <  1:4254724/101‑1 (MQ=18)
                                         agCGCCGCACGGATCGGCCGATGGCAGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCa                                          <  1:2130277/101‑1 (MQ=18)
                                             ccgcACGGATCGGCGGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                      <  2:3321482/101‑1 (MQ=17)
                                             ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                      <  2:1105057/101‑1 (MQ=18)
                                             ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                      <  1:3040680/101‑1 (MQ=18)
                                              cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGGTCCGC.......CCCCGCACCCCCCGCGTATTTTCGCCCAGaaa                                     >  2:801357/1‑101 (MQ=16)
                                              cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCTCCCCCGGCGTATTTGCGCCAAGaaa                                     <  2:4917797/101‑1 (MQ=18)
                                              cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                     <  1:4583735/101‑1 (MQ=18)
                                               gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaa                                    <  2:1962021/101‑1 (MQ=18)
                                               gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaa                                    <  2:4323755/101‑1 (MQ=18)
                                               gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaa                                    <  2:2489664/101‑1 (MQ=18)
                                                cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                   <  1:4154572/101‑1 (MQ=17)
                                                cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCCCCCCCCCGGCGTATTTTCGCCAAGaaaaa                                   >  2:4553042/1‑101 (MQ=16)
                                                      tccgCCGAAGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCTCCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                             <  1:3197574/98‑1 (MQ=12)
                                                      tCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                             >  1:1885418/1‑101 (MQ=17)
                                                      tCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                             <  1:2464376/101‑1 (MQ=18)
                                                       cGGCCGATGGCGGAGAGAAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgggg                            <  2:4653288/101‑1 (MQ=17)
                                                         gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGCTGGGGCTC....CGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcg                          >  1:1365836/1‑101 (MQ=17)
                                                         gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgggggg                          >  2:780250/1‑99 (MQ=17)
                                                         gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcg                          <  2:3213737/101‑1 (MQ=17)
                                                         gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTAATTGCGCCCAGAAAAAACCGGGgcg                          >  1:4682897/1‑101 (MQ=9)
                                                          ccGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgc                         <  2:805713/101‑1 (MQ=17)
                                                          ccGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGGATTTTCGCCCAGAAAAAGCCGGGgcgc                         >  1:3129840/1‑101 (MQ=12)
                                                           cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                        <  2:3404209/101‑1 (MQ=17)
                                                           cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......GGGGCTCCCCCCCCGCACCCCCCGCGGATTTGCGCCCAGAAAAAGACCGGgcgcg                        >  2:1677858/1‑101 (MQ=12)
                                                            gATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcgc                       <  2:4327611/101‑1 (MQ=17)
                                                             aTGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGG....GGGGGCTCCGC.......CCCCCCCCCCCCCGCGTCTTTGCGCCCAGAAAAAACCGGGGCGGGCa                      >  2:345062/1‑101 (MQ=9)
                                                              tGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                     <  1:1143659/101‑1 (MQ=17)
                                                               ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                    <  2:3023837/101‑1 (MQ=17)
                                                                gCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGc                   <  1:3887182/101‑1 (MQ=18)
                                                                   gagaGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCggg                <  1:1482087/101‑1 (MQ=18)
                                                                    agagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCgggg               <  2:3095750/101‑1 (MQ=18)
                                                                    agagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCgggg               <  2:2058113/101‑1 (MQ=18)
                                                                     gagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGc              >  1:4025121/1‑101 (MQ=17)
                                                                      agGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcc             <  2:4964389/101‑1 (MQ=17)
                                                                          aTTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCgg         <  1:25900/101‑1 (MQ=17)
                                                                           tttCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGa        <  1:3365170/101‑1 (MQ=17)
                                                                            ttCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGAt       <  2:4501526/101‑1 (MQ=17)
                                                                               gccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAc    <  2:3783694/101‑1 (MQ=18)
                                                                               gccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAc    <  1:801459/101‑1 (MQ=18)
                                                                                ccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAcc   <  1:1504161/101‑1 (MQ=18)
                                                                                 cgcgCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg  <  1:2044245/101‑1 (MQ=18)
                                                                                 cgcgCAGGCGCGGCGACCCGGGC....GGGGGCTCCGC.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg  <  1:3569662/101‑1 (MQ=18)
                                                                                                    |                                                                                            
TTTTCGGCTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......CGG.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCG  >  NC_014034/2330071‑2330245

Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG