New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 1202951	33 (0.810)	3 (0.080)	3/312	NT	7.9%	coding (780/1089 nt)	xcpY	Type II secretion pathway protein XcpY
	?	AE015451	= 1203076	39 (1.030)					coding (905/1089 nt)	xcpY	Type II secretion pathway protein XcpY

TTTGGGGTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGAGCAGCCTCATGAACCGTGACTGGCTGCAGCGTCATCGCATCACGTTCGCC  >  AE015451/1202890‑1203298                                                                                                                                                                                           |                                                                                                                                                                                                                               tttGGGGTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTc                                                                                                                                                                               >  1:343256/1‑236 (MQ=255)  ttGGGGTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTc                                                                                                                                                                               >  1:629958/1‑235 (MQ=255)  ttGGGGTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTc                                                                                                                                                                               >  1:266687/1‑235 (MQ=255)     gggTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGAt                                                                                                                                                                            <  1:538466/235‑1 (MQ=255)                 gTTGAGTCCGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGc                                                                                                                                                                                                       <  2:165610/196‑1 (MQ=255)                  ttGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCgg                                                                                                                                                                                                        >  1:505389/1‑194 (MQ=255)                  ttGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCt                                                                                                                                                                                               >  1:481693/1‑203 (MQ=255)                     aGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCAc                                                                                                                                                             <  2:266686/234‑1 (MQ=255)                              tGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGga                                                                                                                                                  >  1:427790/1‑236 (MQ=255)                                    cAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGgagggcga                                                                                                                                            >  1:717035/1‑236 (MQ=255)                                                 ggCGCAGCCAGGGCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGcgcc                                                                                                                                <  1:667119/235‑1 (MQ=255)                                                         cAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGcgcc                                                                                                                                <  1:20624/227‑1 (MQ=255)                                                               aTTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGc                                                                                                                                                                     <  2:639000/184‑1 (MQ=255)                                                               aTTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGc                                                                                                                                                                     >  1:639001/1‑184 (MQ=255)                                                                                 ccggCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTgcgc                                                                                                                                 <  2:529311/200‑1 (MQ=255)                                                                                       aGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCCGCGCCTGgagg                                                                                                                                                >  2:520897/1‑181 (MQ=255)                                                                                                cACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGc                                                                                                                                                               <  1:47063/157‑1 (MQ=255)                                                                                                 aCGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTGGGCACCTGCGCCTGgaggg                                                                                                                                               >  2:282145/1‑172 (MQ=255)                                                                                                   gcgGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTGCTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAgacctggctgcgccagagttgcgcc                                                                                                                                                                                                       >  2:242943‑M2/1‑89 (MQ=255)                                                                                                      gCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGc                                                                                                                                                               >  1:481129/1‑151 (MQ=255)                                                                                                      gCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGc                                                                                                                                                               <  2:481128/151‑1 (MQ=255)                                                                                                        acaGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCg                                                                                                                                                                                                         >  1:285200/1‑107 (MQ=255)                                                                                                        acaGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCg                                                                                                                                                                                                         <  2:285199/107‑1 (MQ=255)                                                                                                        acaGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCg                                                                                                                                                                                                         >  1:757031/1‑107 (MQ=255)                                                                                                        acaGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCg                                                                                                                                                                                                         <  2:757030/107‑1 (MQ=255)                                                                                                                  aaGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCCCCTGCGCCTGGAGGGCGAGGGCAGCGCGCCGCCATGGCCTGATATggcg                                                                                                             >  2:128732/1‑189 (MQ=255)                                                                                                                        cTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTTGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCGAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGt                                                                                                                                     <  1:177463/159‑1 (MQ=255)                                                                                                                         tGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCAt                                                                                                                           >  1:273849/1‑168 (MQ=255)                                                                                                                         tGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCAt                                                                                                                           <  2:273848/168‑1 (MQ=255)                                                                                                                           cgcgAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTgg                                                      <  1:111672/235‑1 (MQ=255)                                                                                                                            gcgAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGa                                                    <  1:421269/236‑1 (MQ=255)                                                                                                                                                caACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAgacctggctgcgccagagttgcgcctgacgccattgctgactcaaccacaggccaccccaaacggtagccagcaccaggcaagctgccagcagccgctgctgctggcgggaggcggccggcaacga                                                                                                  <  1:11415‑M2/170‑127 (MQ=255)                                                                                                                                                caACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAgacctggctgcgccagagttgcgcctgacgccattgctgactcaaccacaggccaccccaaacggtagccagcaccaggcaagctgccagcagccgctgctgctggcgggaggcggccggcaacga                                                                                                  >  2:11415‑M2/1‑44 (MQ=255)                                                                                                                                                caACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCt                                                                                                          >  1:686368/1‑162 (MQ=255)                                                                                                                                                                aGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGgag                                                                                                                                                 <  2:269907/107‑1 (MQ=255)                                                                                                                                                                aGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGgag                                                                                                                                                 >  1:269908/1‑107 (MQ=255)                                                                                                                                                                 gCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGGGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATggcggcgtg                                                                                                        >  2:87846/1‑144 (MQ=255)                                                                                                                                                                   tAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGGTCAAGATGGc                                                                         >  1:234483/1‑176 (MQ=255)                                                                                                                                                                        gacCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGAGCAGCCTCATGAACCGTGACTGGCTGCAGCGTCATCGCATCACg        >  1:652277/1‑236 (MQ=255)                                                                                                                                                                             gCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATggcgggcgcc                                                                                                       >  2:213851/1‑131 (MQ=255)                                                                                                                                                                               aGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGAGCAGCCTCATGAACCGTGACTGGCTGCAGCGTCATCGCATCACGTTCGcc  >  1:398511/1‑235 (MQ=255)                                                                                                                                                                                      cTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGAGCAGcc                                              <  1:442941/184‑1 (MQ=255)                                                                                                                                                                                       ttGCAgacctggctgcgccagagttgcgcctgacgccattgctgactcaaccacaggccaccccaaacggtagccagcaccaggcaagctgccagcagccgctgctgctggcggggggcggcccgcaa                                                                                                     <  2:139938‑M2/128‑124 (MQ=255)                                                                                                                                                                                         gCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGGGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATggcg                                                                                                             >  2:73210/1‑118 (MQ=255)                                                                                                                                                                                           |                                                                                                                                                                                                                               TTTGGGGTGGCCTGTGGTTGAGTCAGCAATGGCGTCAGGCGCAACTCTGGCGCAGCCAGGTCATTGCCGTGACCGGGGAGCAGGCCAGCCCTCGGCACGCGGCACAGGCCCTCAAGCGCCTGCGCGAGAGCGTACTGCAGCAGCAACTGCGTACACGTCAGCTAGACGACCTGCAGGCTCGCTTGCAGACCTGGCTGCGTGACAACCCCGGCTTGCGCCTGCAAGCGGTGCGCTTCGATGGTCAGCGTTGGCACCTGCGCCTGGAGGGCGAGGGCAGTGCGCCGCCATGGCCTGATATGGCGGCTGCCGCTGGCGCCACAGTGCAGGTTCAAGATGGCCAAGTGATCTTCGACCTGGGAGCAGCCTCATGAACCGTGACTGGCTGCAGCGTCATCGCATCACGTTCGCC  >  AE015451/1202890‑1203298

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ 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.