New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2808593	44 (0.810)	3 (0.060)	3/250	NT	6.6%	pseudogene (278/1178 nt)	ygaY	putative transporter YgaY, N‑terminal fragment
	?	NC_000913	= 2808601	43 (0.840)					pseudogene (286/1178 nt)	ygaY	putative transporter YgaY, N‑terminal fragment

GTTCGGCAGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTC  >  NC_000913/2808452‑2808735                                                                                                                                              |                                                                                                                                                gTTCGGCAGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGAGTGTCTCGATGACCTTACTGGCGGCAGGTAGATAACCGCcagca                                                                                                                                                >  2:913600/1‑143 (MQ=255)      gCAGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGcagtcag                                                                                                                                           >  1:256861/1‑143 (MQ=255)      gCAGGCTTTATTGTTACCGCCGCGCAGTTGGGCTAGGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGTAATGATTGAACTGTGCAGGCAGATTGTGTCGATGACCTTACTGGCGGCATGTTGATTGCCGCCAGCggccag                                                                                                                                           >  2:321091‑M1/1‑137 (MQ=255)        aGGCGTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCagtcagtc                                                                                                                                         <  1:138088/143‑1 (MQ=255)           cTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTCAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCgct                                                                                                                                      >  1:960675‑M2/1‑140 (MQ=255)            gtnaTTGTCGCCGCCCCGNCGTTGGGCTATGCCGCACGTCTACTGNTGCTTGTTCCCCTCGGTGATATGTTTGGACGCCGCCGCCTGTTTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCgctg                                                                                                                                     >  2:162226‑M2/2‑139 (MQ=255)             ttATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCgactgactgctgg                                                                                                                                    <  1:900440‑M1/143‑14 (MQ=255)               aTTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCTAGTACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCgctggcg                                                                                                                                  >  1:179200‑M2/1‑136 (MQ=255)                   ttACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGACCGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCgatga                                                                                                                              >  1:446868/1‑143 (MQ=255)                       cgccgcGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCgatgatgat                                                                                                                          <  1:334959/143‑1 (MQ=255)                         ccgcGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATcc                                                                                                                        >  2:84004/1‑143 (MQ=255)                            cgcgGTTGGGCTGTGCTGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTTGTTGTCTATGATGATCCTCg                                                                                                                     <  2:382552/143‑1 (MQ=255)                               cgcgggccTATGCCGCCGGCCTACTGTTTCCCGTTCCCCTCGGTGCCATGTTTTGCCGCCGCCGCCTGATCGTTGCTATGACTTTACCGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTa                                                                                                                  <  2:869424/136‑1 (MQ=255)                                 ttGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGCGATATGTGTGACCGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATAACGGCCAGCGGTCAGCAGCTGGCGATGGTGACCGCCGGTACg                                                                                                                >  2:597427/1‑143 (MQ=255)                                  tGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACgg                                                                                                               <  1:749363/143‑1 (MQ=255)                                    ggCTATGCCTCAGTGCTACTGTTTCTTGTGCCCCGCGGTAATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCAAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCa                                                                                                             <  2:431883/143‑1 (MQ=255)                                           ccGCGGGTCTACTGTTTGTTGTTCCCCTGGCTGATATGTTTGACCGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCg                                                                                                      <  2:944489/143‑1 (MQ=255)                                           ccGCAGGTCCACTGTTTCTTGTTCCGCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCg                                                                                                      <  2:945623/143‑1 (MQ=255)                                             gCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATAGGTTTGAGCGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGt                                                                                                    <  1:4304/143‑1 (MQ=255)                                              cAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGtt                                                                                                   <  1:1017304/143‑1 (MQ=255)                                              cAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGtt                                                                                                   <  1:267074/143‑1 (MQ=255)                                                     aCTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATtctc                                                                                            <  1:368778/143‑1 (MQ=255)                                                     aCTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGATTATgctc                                                                                            >  2:21584/1‑143 (MQ=255)                                                      cTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCgactgactgctggcggtaatcaa                                                                                                                          >  2:555317‑M1/1‑89 (MQ=255)                                                      cTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCgactgactgctggcggtaatcaa                                                                                                                          <  1:555317‑M1/112‑24 (MQ=255)                                                      cTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCCTTAACCGGTCTATcctcc                                                                                           >  2:612851/1‑142 (MQ=255)                                                          ttCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACAGGCTTATTCTCAGTCg                                                                                       >  2:139138/1‑143 (MQ=255)                                                            cTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCCCAGTCGTg                                                                                     <  1:728774/143‑1 (MQ=255)                                                                      tCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTc                                                                           <  1:84004/143‑1 (MQ=255)                                                                       cGGTGATATGTTTGAACGCCGCCGCCTGATTGTCGCGATGACCTGACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCt                                                                          <  1:616500/143‑1 (MQ=255)                                                                        ggcgATATGTTTGAACGCCGCCGCCTGAGTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTg                                                                         <  1:584983/140‑1 (MQ=255)                                                                          tGATATGTTTGGACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGt                                                                       <  2:411514/143‑1 (MQ=255)                                                                            atatGCTGGAGCGCCGCCGCCTGATTGCCTCGATGACCTGACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGTTCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTc                                                                     <  1:32009/143‑1 (MQ=255)                                                                                 tttGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTg                                                                >  1:825628/1‑143 (MQ=255)                                                                                      aCGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGCTTACCGCCAGCAGTCAGTCGCTGGCGCTGATGATCCTCGGTCCGGCCTTAACCGGTTTATTCTCAGTCGTGGCACACCTTCTGGTTCCGCTGGCAGc                                                           >  2:910367/1‑143 (MQ=255)                                                                                        gccgccgccTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGGTGGCGCTGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCCGTAGTGGCACAACGTCTAGAGCCGCTCGCCGCGa                                                         >  2:506285/1‑143 (MQ=255)                                                                                         ccgccgccTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGCTGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGTGAc                                                        >  1:267850/1‑143 (MQ=255)                                                                                              gccGGATGGTCTCGCTGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTg‑g                                                  <  2:841804/143‑1 (MQ=255)                                                                                                cTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCt                                                <  1:136892/143‑1 (MQ=255)                                                                                                    ttGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCAc                                            >  1:333475/1‑143 (MQ=255)                                                                                                      gTCTCGATGACCTTACTGGCGGCATGTTGATGACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCg                                          <  1:303132/143‑1 (MQ=255)                                                                                                       tctcGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTccccag                                         >  2:111028/1‑141 (MQ=255)                                                                                                         tcGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCgggt                                       >  1:638261/1‑141 (MQ=255)                                                                                                               tccTTACTGGTGGCATGTTTATTACCGCCAACAGGCAGTCGCTGGCGATGATGATCCGCGGTAGGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAAcgc                                 <  1:313572/142‑1 (MQ=255)                                                                                                               aCCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCATCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCAGAAATTCTGGTTCAGCTGGAAGC‑TCGCCGCGCTTCTCCGGATaagtcc                                 >  1:954685/1‑139 (MQ=255)                                                                                                                   tACTGGCTGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCTGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCa                             <  1:337657/143‑1 (MQ=255)                                                                                                                      tGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGGTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAg                          >  1:895485/1‑143 (MQ=255)                                                                                                                      tGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGCTCCGCTGACAGCGACGCTG‑ACTTCACCGGATAAACGCGGCAAAg                          >  2:88599/1‑143 (MQ=255)                                                                                                                            cATGTTCATTCCCGCGCGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTg                    <  2:138844/143‑1 (MQ=255)                                                                                                                               gTTGATTCCCGCGCGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCa                 <  2:256861/143‑1 (MQ=255)                                                                                                                                ttGATTACCGCCAGCAGTCAGTCgctggcggtaatcaacatgccgccagtaaggtcatcgagacaatcaggcggcggcgttcaaacatatcaccgaggggaacaagaaacag                                                >  2:555317‑M2/1‑23 (MQ=255)                                                                                                                                ttGATTACCGCCAGCAGTCAGTCgctggcggtaatcaacatgccgccagtaaggtcatcgagacaatcaggcggcggcgttcaaacatatcaccgaggggaacaagaaacag                                                <  1:555317‑M2/112‑90 (MQ=255)                                                                                                                                   aTTACCGCCAGCAGTCAGTCGCTGGCGATGATTATCCGCGTTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAACCGCGGCAAAGTGGTTGGCACcat             >  2:380108/1‑143 (MQ=255)                                                                                                                                        cGCCAGCgactgactgctggcggtaatcaacatgccgccagtaaggtactagagacaatcaggcggcggcgttcaaacatatcaccgaggggaacaagaaacagtagacctgcggcatagcccaactgcgcggcggtaacaat         >  1:179200‑M1/1‑7 (MQ=255)                                                                                                                                        cGCCAGCAGTCAGTCGCTGGCGATGGTGATCCTCGGTACGGCAGTAACCGGTTTATTCTCAGTCGTGGCACACATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGa        <  2:439345/143‑1 (MQ=255)                                                                                                                                          ccAGCAGTCAGTCgctggcggtaatcaacatgccgccagtaaggtcatcgagacaatcaggcggcggcgttcaaacatatcaccgaggggaacaagaaacagtagacctgcggcatagcccaactgcgcggcggtaacaataa       <  1:900440‑M2/143‑131 (MQ=255)                                                                                                                                           cAGCgactgactgctggcggtaatcaacatgccgccagtaaggtcatcgagacaaacaggcggcggcgtccaaacatatcaccgaggggaacaagcancagtagacgtgcggcatagcccaacgncggggcggcgacaatnac      >  2:162226‑M1/1‑4 (MQ=255)                                                                                                                                            aGCgactgactgctggcggtaatcaacatgccgccagtaaggtcatcgagacaatcaggcggcggcgttgaaacatatcaccgaggggaacaagaaacagtagacctgcggcatagcccaactgcgcggcggtaacaataaag     >  1:960675‑M1/1‑3 (MQ=255)                                                                                                                                              cagtcagtCGCGGGCGATGATGAGCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTc  <  1:217235/143‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                GTTCGGCAGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTC  >  NC_000913/2808452‑2808735

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.