New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3114511	NA (NA)	3 (0.070)	3/250	NT	NA	intergenic (‑159/+39)	pppA/yghJ	prepilin peptidase/putative lipoprotein YghJ
	?	NC_000913	= 3114541	NA (NA)					noncoding (29/34 nt)	other	REP219c

TCCGTCCTACGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTGGCTCACACCGCCCTCGAAGCTCATCTCGCTCG  >  NC_000913/3114403‑3114683                                                                                                                                           |                                                                                                                                               tCCGTCCTACGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATCCCGGATGCGGCGCGAGCGCCTTATCCGGCccac                                                                                                                                            <  1:880079‑M2/143‑5 (MQ=255) tCCGTCCTACGGATGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCCAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATCCGGCGCGAGCGCCTTACCCGGCCtgc                                                                                                                                            >  1:180881/1‑141 (MQ=255)  ccGTCCTGCGGGTGTCTGCCCGCGCTAATACTCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACg                                                                                                                                           <  2:5816/143‑1 (MQ=255)   cGTCCTACGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACgg                                                                                                                                          <  1:199300/143‑1 (MQ=255)     cccTGCGGGTGTCTGCCAGCGGAAATAATCGCGGCGTTCCCCGTGTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGc                                                                                                                                        <  2:129112/142‑1 (MQ=255)       ctccGGGTGTCTGCCAGCGCAAATAGTCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCtt                                                                                                                                      <  1:672077/140‑1 (MQ=255)        tACGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGCGCGCCTTATCCGGCCTACGGGCTTa                                                                                                                                     >  1:225096/1‑143 (MQ=255)         aCGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTAc                                                                                                                                    >  1:677701/1‑143 (MQ=255)           gggTGTCGGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTc                                                                                                                                  <  1:274144/143‑1 (MQ=255)             gtgtCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGCCCAGCTCCGATGGTAGTGCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCgg                                                                                                                                <  1:213782/143‑1 (MQ=37)                 cgaccAGCTTAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGa                                                                                                                            <  2:806036/140‑1 (MQ=255)                     cAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATc                                                                                                                        <  2:629840/143‑1 (MQ=255)                           aaaTAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGTAGACGTCTTATGc                                                                                                                  >  1:62447/1‑143 (MQ=255)                            aataatCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTACCCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCt                                                                                                                 <  2:783215/143‑1 (MQ=255)                            aataatCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTAGTCGGCAGACCTCTTATGcc                                                                                                                 >  2:766442/1‑142 (MQ=255)                                 tCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGGGCCTTATCCGGCCTACGGGCTTACTCGGCGGGCATCTTCTGCTCGGTa                                                                                                            >  1:600612/1‑143 (MQ=255)                                 tCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACACCTTATGCTCGGtg                                                                                                            >  2:364281/1‑142 (MQ=255)                                  cgcgGCTTGCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTaa                                                                                                           <  2:727576/143‑1 (MQ=255)                                   gcgGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATCCGGCGCGCCCGCCTTATCCCGCCCACGGGCTTCCTCTGCAGACGTCCTCTGCTCgctcac                                                                                                          >  1:907765/1‑138 (MQ=255)                                            cccGGCTGTAGCCCCGGTGAGCAGGCGCATCGGGCAAATGTGTTATCCCGGTGCGCCTTATTTCGTGCCGGATGCGGCGCGAGCGCCTTATCCGGTCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAAt                                                                                                 <  2:713192/143‑1 (MQ=38)                                                 cTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGCCAGACATCTTATGCTCGGTAACCTGATTGATGGttt                                                                                            >  2:848390/1‑143 (MQ=255)                                                  tGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTc                                                                                           <  1:489817/143‑1 (MQ=255)                                                    tAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTACCCGGCCTACGGGCTTACTCGGAAGACATCTTATGCTCGGTAACCTGATTCATGGTTTCCg                                                                                         >  2:502778/1‑143 (MQ=255)                                                      ggCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGt                                                                                       <  1:778666/143‑1 (MQ=255)                                                       gCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGGGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTc                                                                                      <  2:426442/143‑1 (MQ=255)                                                        cccGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTCTTTCATGCCGGATGCGGCGCGAGCGCCTTCTCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTCATGGTCTCCAGTcc                                                                                     >  2:76844/1‑143 (MQ=39)                                                              aaGCAGGCGCACCGGGCAAATGTGTTAACCCGGTGCGCCCTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTGCGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTc                                                                               <  1:566562/143‑1 (MQ=255)                                                               aGCGGGCGCATCGGGCAAATGTGTTCACCCGGTCCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTcc                                                                              <  2:543733/143‑1 (MQ=255)                                                                gCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTGATGTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCg                                                                             <  2:571086/143‑1 (MQ=255)                                                                 cAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCgc                                                                            >  2:883519/1‑142 (MQ=255)                                                                 cAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACACCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCGCGTTCCgg                                                                            >  2:540134/1‑143 (MQ=255)                                                                  aGGCGCATCGGGCAGATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGt                                                                           <  2:67492/143‑1 (MQ=255)                                                                   ggCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTCCCGGtt                                                                          >  1:73316/1‑143 (MQ=255)                                                                    gcgcATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGGTTAATGGTTTCCCGCCCCTGCTCCGGtct                                                                         >  1:919082/1‑141 (MQ=255)                                                                        aTCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGc                                                                     >  2:383196/1‑143 (MQ=255)                                                                            ggCAAATGTGTTCACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCt                                                                                                                       <  1:493074/89‑1 (MQ=255)                                                                            ggCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCt                                                                                                                       >  2:493074/1‑89 (MQ=255)                                                                               aaaTGTGTTAACCATGTGCGCCGGAGTTCAGGCCGGAGGCGGCGCGAGCGCCTTATCCGTCCTACGTGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCTGTCCCTGTTCCTGTTTCGGCAGATCGa                                                              <  1:242345/143‑1 (MQ=255)                                                                                   gtgtTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGa                                                          <  1:626452/143‑1 (MQ=255)                                                                                    tgtTCACCCGGTGCGCCTTATTTCATGCCGTATGCGCCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGAc                                                         <  2:893148/143‑1 (MQ=255)                                                                                     gtTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTGCTCGGCAGGCATCTTGTGGTCGGTAACCTGATTAATGGTTTGCGGTCCCTGTTCCGGTTTCGGGAGGTCGGGTGAcg                                                        >  1:722529/1‑143 (MQ=38)                                                                                     gtTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGACCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCCTATGCTCGGGAACCTGATTAATAGTTTCCGGTCCCTGCTCCGGCTACGGCAGATCGAgcggcg                                                        >  2:648865/1‑138 (MQ=38)                                                                                      ttAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGAcgc                                                       >  2:602116/1‑143 (MQ=255)                                                                                        aaCCCGGTGCGCCTTATTTCACGCCGGAGGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGa                                                     <  2:40142/143‑1 (MQ=255)                                                                                                         ttCGTGCGGGATGGCGCTCGCGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAAGGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGAc                                    <  2:557755/143‑1 (MQ=255)                                                                                                          tCATTCCGGATGCGGGTTGAGTGCCTTATCCGGCCTCCTGGCTTACTCGGCTGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTGCGCTCTTGGTGGATCGATAGACTCGAGCGTGTTGTAAGCCGACt                                   <  2:289857/143‑1 (MQ=255)                                                                                                            aTGCCGGATGCGGCGCGAGCGCCTTATCCGGCatgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttatcgggcctacagacggggaaagccgcgattatttgcgctggcagacacccgtaggacggata                                 <  1:234080‑M2/143‑112 (MQ=255)                                                                                                            aTGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTgg                                 >  1:111609/1‑143 (MQ=255)                                                                                                               ccGGATGCGGCGCGGGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTACTGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTGGCTc                              <  1:826086/143‑1 (MQ=255)                                                                                                                cGGATGCGGCGCGAGCGCCTTATCCGGCatgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttatcgg                                                                                           <  2:97204‑M2/81‑54 (MQ=255)                                                                                                                cGGATGCGGCGCGAGCGCCTTATCCGGCatgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttatcgg                                                                                           >  1:97204‑M2/1‑28 (MQ=255)                                                                                                                cGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGCCTGGCTca                             >  1:785056/1‑143 (MQ=255)                                                                                                                cGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGGGTTGTAAGCCGACCGGcccc                             >  1:177068/1‑140 (MQ=255)                                                                                                                                gcCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTCGTAAGCCGACTGGCTCACCCCGCCCTCGACGCt             >  1:600331/1‑143 (MQ=255)                                                                                                                                      tCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTGGCTCACACCGCCCTCGAAGCTCAtcgc       >  1:342549/1‑141 (MQ=255)                                                                                                                                       ccGGCatgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttattgggcctacagacggggcaagccgcgattatttgcgctggcagacacccgtaggacggataaggcgttttacgccgcatccagcaaga      <  2:638980‑M2/143‑139 (MQ=255)                                                                                                                                       ccGGCCGTCGGGCTGACTGGGCAGATCTCTTATGCTCGGTACCCGTATTAATGGTTTCCGGTTCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTGGCTCACACCGCCCTCGAAGCTCATctcg      <  2:131459/143‑1 (MQ=255)                                                                                                                                        cGGCatgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttatcgggcctacagacggggaaagccgcgattatttgcgctggcagacacccgtaggacggataaggcgtgttacgccgcatccagcaagtt     <  2:592869‑M2/143‑140 (MQ=255)                                                                                                                                           catgaaataaggcgcaccgggttaacacatttgcccgatgcgcctgcttatcgggcctacagacggggaaagccgcgattatttgcgctggcagacacccgtaggacggataaagcggtttacgccgcatccgccaagttaca  <  1:230495‑M2/143‑143 (MQ=255)                                                                                                                                           |                                                                                                                                               TCCGTCCTACGGGTGTCTGCCAGCGCAAATAATCGCGGCTTTCCCCGTCTGTAGGCCCGATAAGCAGGCGCATCGGGCAAATGTGTTAACCCGGTGCGCCTTATTTCATGCCGGATGCGGCGCGAGCGCCTTATCCGGCCTACGGGCTTACTCGGCAGACATCTTATGCTCGGTAACCTGATTAATGGTTTCCGGTCCCTGTTCCGGTTTCGGCAGATCGAGTGACGCGAGCGTGTTGTAAGCCGACTGGCTCACACCGCCCTCGAAGCTCATCTCGCTCG  >  NC_000913/3114403‑3114683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.