New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	6049480 =	33 (1.280)	3 (0.120)	3/302	NT	9.2%	coding (342/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase
	?	AE015451	6049563 =	28 (1.140)					coding (425/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase

GCCGCAGTGGCGAGCCCTACGTGACCCACCCGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCT  >  AE015451/6049254‑6049697                                                                                                                                                                                                                                   |                                                                                                                                                                                                                          gccgcAGTGGCGAGCCCTACGTGACCCACCCGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCgg                                                                                                                                                                                                                    <  2:422195/234‑1 (MQ=255)     cAGTGGCGAGCCCTACGTGACCCACCCGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGaaaa                                                                                                                                                                                                                >  2:279916/1‑234 (MQ=255)           cGAGCCCTACGTGACCCACCCGCGGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCaga                                                                                                                                                                                                        <  1:292723/236‑1 (MQ=255)                  tACGTGACCCACCCGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGatggc                                                                                                                                                                                                 >  1:119718/1‑236 (MQ=255)                        gcggttgccgcgcgcgctcttcactgcacgatgaatcagcgacgagcgcatcgggtgcatggccttgaagccaaggtcttcgaactctacgcgcacggtgtgcatccccaggcggtttgcgatgggggcgtagatctcgagggtttccttggcaatgcgccggcgcttttcgccagacagcacttccagggtgcgcatgttgtGCAGGCGGaa                                                                                                                                                                                                                  >  2:286173‑M1/204‑213 (MQ=255)                               cGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGCCAGCAAGCTGACCCAGATGAAGTTCGAGACCAAGGCCGAGGCGCAGGc                                                                                                                                                                                                                      >  1:11928/1‑202 (MQ=255)                                cgcgcgcgctcttcactgcacgatgaatcagcgacgagcgcatcgggtgcatggccttgaagccaaggtcttcgaactctacgcgcacggtgtgcatccccaggcggtttgcgatgggggcgtagatctcgagggtttccttggcaatgcgccggcgcttttcgccagacagcacttccagggtgcgcatgttgtGCAGGc                                                                                                                                                                                                                      <  2:296537‑M1/6‑1 (MQ=255)                                      cGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGatggccatggccat                                                                                                                                                                                        >  1:447239/1‑225 (MQ=255)                                       gTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCaga                                                                                                                                                                                                        <  2:375676/208‑1 (MQ=255)                                       gTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCaga                                                                                                                                                                                                        >  1:375680/1‑208 (MQ=255)                                                             cgcgacgagcgcatcgggtgcatggccttgaagccaaggtcttcgaactctacgcgcacggtgtgcatccccaggcggtttgcgatgggggcgtagatctcgagggtttccttggcaatgcgccggcgcttttcgccagacagcacttccagggtgcgcatgttgtGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGa                                                                                                                                                                               >  2:173304‑M1/167‑211 (MQ=255)                                                                  aTGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACt                                                                                                                                                                                                              >  1:79024/1‑175 (MQ=255)                                                                             gagCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGcaca                                                                                                                                      >  1:482721/1‑236 (MQ=255)                                                                                 cTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACAt                                                                                                                                  <  1:437841/236‑1 (MQ=255)                                                                                   gATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCa                                                                                                                                                                                                                         <  1:191120/147‑1 (MQ=255)                                                                                      ggcggcCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATcc                                                                                                                                                                          <  1:37163/191‑1 (MQ=255)                                                                                           ccATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGatggcc                                                                                                                                                                                                >  2:209394/1‑164 (MQ=255)                                                                                             aTGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTg                                                                                                                                                               >  2:311749/1‑195 (MQ=255)                                                                                                      gATGGGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGc                                                                                                                 <  2:119714/232‑1 (MQ=255)                                                                                                           gATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCcg                                                                                                                                                                                  >  2:167083/1‑162 (MQ=255)                                                                                                              cGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCg                                                                                                        >  2:175647/1‑233 (MQ=255)                                                                                                                        ggCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGGCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAATATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGc                                                                                                                                                        >  1:278883/1‑175 (MQ=255)                                                                                                                         gCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGgc                                                                                            <  2:482717/234‑1 (MQ=255)                                                                                                                            tgcatccccaggcggtttgcgatgggggcgtagatctcgagggtttccttggcaatgcgccggcgcttttcgccagacagcacttccagggtgcgcatgttgtGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTg                                                                                                                                                                     >  2:337520‑M1/104‑158 (MQ=255)                                                                                                                            tgcatccccaggcggtttgcgatgggggcgtagatctcgagggtttccttggcaatgcgccggcgcttttcgccagacagcacttccagggtgcgcatgttgtGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTg                                                                                                                                                                     <  1:337524‑M1/55‑1 (MQ=255)                                                                                                                             cGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGTTCGAGGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAg                                                                                                   <  1:34562/223‑1 (MQ=255)                                                                                                                               ccAAGGAGGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGa                                                                                                                                                 <  1:461438/175‑1 (MQ=255)                                                                                                                                             agccagcAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTc                                                                        >  1:296541/1‑234 (MQ=255)                                                                                                                                                       ttGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCg                                                                                                        >  1:44476/1‑192 (MQ=255)                                                                                                                                                           cGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGatat                                                                                                                                                                            >  1:387292/1‑120 (MQ=255)                                                                                                                                                             agaCCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATc                                                      <  1:279920/236‑1 (MQ=255)                                                                                                                                                                ccGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCAt                                                                                        >  2:406963/1‑199 (MQ=255)                                                                                                                                                                    ggCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAAcc                                               <  1:209398/236‑1 (MQ=255)                                                                                                                                                                      ccGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGc                                             <  1:311753/236‑1 (MQ=255)                                                                                                                                                                            tGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGc                                             <  1:408848/230‑1 (MQ=255)                                                                                                                                                                                 gATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGc                                   >  1:439970/1‑235 (MQ=255)                                                                                                                                                                                    ggggTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAAccc                                                                          <  2:194561/193‑1 (MQ=255)                                                                                                                                                                                                          tGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGAt                                     <  2:396759/208‑1 (MQ=255)                                                                                                                                                                                                                 cGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCt  <  1:175651/236‑1 (MQ=255)                                                                                                                                                                                                                                 gcgcAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGAc         <  2:240116/213‑1 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                          GCCGCAGTGGCGAGCCCTACGTGACCCACCCGCTGGCCGTGGCCAGCATCCTCGCCGACATGCACATGGACCATCAGAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCT  >  AE015451/6049254‑6049697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ 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.