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

AGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTG  >  NC_000913/2808459‑2808737                                                                                                                                               |                                                                                                                                          aGGCGTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCagtcagtc                                                                                                                                           <  1:138088/143‑1 (MQ=255)    cTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTCAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCgct                                                                                                                                        >  1:960675‑M2/1‑140 (MQ=255)     gtnaTTGTCGCCGCCCCGNCGTTGGGCTATGCCGCACGTCTACTGNTGCTTGTTCCCCTCGGTGATATGTTTGGACGCCGCCGCCTGTTTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCgctg                                                                                                                                       >  2:162226‑M2/2‑139 (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)                                               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)                                                                                                                                 cGCCAGCAGTCAGTCGCTGGCGATGGTGATCCTCGGTACGGCAGTAACCGGTTTATTCTCAGTCGTGGCACACATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGa          <  2:439345/143‑1 (MQ=255)                                                                                                                                   ccAGCAGTCAGTCgctggcggtaatcaacatgccgccagtaaggtcatcgagacaatcaggcggcggcgttcaaacatatcaccgaggggaacaagaaacagtagacctgcggcatagcccaactgcgcggcggtaacaataa         <  1:900440‑M2/143‑131 (MQ=255)                                                                                                                                       cagtcagtCGCGGGCGATGATGAGCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTc    <  1:217235/143‑1 (MQ=255)                                                                                                                                         gtcagtcGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTctg  <  1:612851/143‑1 (MQ=255)                                                                                                                                          ctggccgctggcggcaatcaacatgccgccagtaaggtcatcgacacaatctgcctgcacagttcaatcattacaccgaggggaacaagaaacagtagacctgcggcctagcccaactgcgcggcggtaacaataaagcctgc  >  2:321091‑M2/6‑6 (MQ=255)                                                                                                                                               |                                                                                                                                          AGGCTTTATTGTTACCGCCGCGCAGTTGGGCTATGCCGCAGGTCTACTGTTTCTTGTTCCCCTCGGTGATATGTTTGAACGCCGCCGCCTGATTGTCTCGATGACCTTACTGGCGGCATGTTGATTACCGCCAGCAGTCAGTCGCTGGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTG‑GCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTG  >  NC_000913/2808459‑2808737

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.