New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 5337245	32 (0.780)	3 (0.080)	3/322	NT	8.7%	coding (695/1443 nt)	PP_4696	Nitrogen regulation protein NR(I)
	?	AE015451	= 5337247	32 (0.820)					coding (697/1443 nt)	PP_4696	Nitrogen regulation protein NR(I)

CCCATGCAGGACATGTACAGCAAGATCCGCAAGGTCGCGCCTACCGACTCCAATGTGCTGATCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGACCTGAAAAACCTGGCCAAGGCCGGCCAGTTCCGTGAAG  >  AE015451/5337022‑5337472                                                                                                                                                                                                                                |                                                                                                                                                                                                                                    cccATGCAGGACATGTACAGCAAGATCCGCAAGGTCGCGCCTACCGACGCCAATGTGCTGATCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGTCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGgc                                                                                                                                                                                                                          <  1:60476/235‑1 (MQ=255)                       aGATCCGCAAGGTCGCGCCTACCGACTCCAATGTGCTGATCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGgccg                                                                                                                                                                                                     >  2:478268/1‑234 (MQ=255)                             gCAAGGTCGCGCCTACCGACTCCAATGTGCTGATCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGc                                                                                                                                                                                                                  >  2:521750/1‑215 (MQ=255)                                                              tCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTg                                                                                                                                                            >  1:669407/1‑236 (MQ=255)                                                                cAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAgcgccggtgaacgcgcctttttcgtggccgaacagttcggattcgatcagcgtttc                                                                                                                                                                           >  1:646708‑M2/1‑163 (MQ=255)                                                                   ggCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGcc                                                                                                                                                          <  2:687772/233‑1 (MQ=255)                                                                          cGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGc                                                                                                                                                           >  1:339494/1‑225 (MQ=255)                                                                                 cGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCt                                                                                                                                          <  1:478269/235‑1 (MQ=255)                                                                                      aaGAGCTGGTGGCCCGCGCCCTGCACAGCCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCct                                                                                                                                     <  1:117050/235‑1 (MQ=255)                                                                                                ggCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCGGCGtgtg                                                                                                                           >  1:177115/1‑235 (MQ=255)                                                                                                 gCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGa                                                                                                                                                                                                 >  1:366864/1‑164 (MQ=255)                                                                                                        cccTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGa                                                                                                                   <  1:521751/235‑1 (MQ=255)                                                                                                                             gtgccAAGGAACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAgcgccggtgcacgcgcctttttcgtggccgaacagttcggattcg                                                                                                                                                                                      >  1:357134‑M2/3‑102 (MQ=255)                                                                                                                                   aGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGGTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAg                                                                                                                     >  1:71802/1‑206 (MQ=255)                                                                                                                                              atCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGc                                                                                                                                                        <  2:439598/160‑1 (MQ=255)                                                                                                                                                       caCTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCtgctgc                                                                                                                                <  2:177114/174‑1 (MQ=255)                                                                                                                                                        aCTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGAtgt                                                                   >  1:450814/1‑235 (MQ=255)                                                                                                                                                                gCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGCAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGAtcc                                                                                                        >  2:465032/1‑188 (MQ=255)                                                                                                                                                                 ccATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGAt                                                                                                          <  2:722754/187‑1 (MQ=255)                                                                                                                                                                 ccATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGAt                                                                                                          >  1:722755/1‑187 (MQ=255)                                                                                                                                                                   aTCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAGGGGCGCGTTCACCGGCGCCAgcgccggtgaacgcgcctt                                                                                                                                                                                                                >  2:506405‑M2/1‑64 (MQ=255)                                                                                                                                                                    tCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCCCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGCAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGcg                                                                                                                                      >  1:101126/1‑155 (MQ=255)                                                                                                                                                                         gAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCtggcgccggtgaacgcgcctttttcgtggccgaacagttcggattcgatcagcgtttcggggatggccgcgcagttcaccgagatcatcggtgccttggcccggcgagacaggttgtgcagggcgcgggccaccagctctttaccggtgcccgactcgccctg                                                                  >  1:646708‑M1/1‑56 (MQ=255)                                                                                                                                                                              gCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCTGGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTCGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCaaaa                                                                            >  1:651554/1‑204 (MQ=255)                                                                                                                                                                                  aTCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCACCTGATCGCCGCGACCCACcg                                           <  2:669406/233‑1 (MQ=255)                                                                                                                                                                                    cGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTgc                                                                 >  2:428097/1‑209 (MQ=255)                                                                                                                                                                                    cGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTGCACCGGCGCtggcgccggtgaacgcgcctttttcgtggccgaacagttcggattcgatcagcgtttcggggatggccgcgcagttcaccgagatcatcggttccttggcac                                                                                                                               >  1:357134‑M1/1‑45 (MQ=255)                                                                                                                                                                                     gAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGGAGGTTCGGTGCAGTCGCa                                                                               >  2:202636/1‑194 (MQ=255)                                                                                                                                                                                          cGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAACAGGTCGAtgt                                                                   >  2:690048/1‑201 (MQ=255)                                                                                                                                                                                           gAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGACCTGaacaa                               >  1:665927/1‑236 (MQ=255)                                                                                                                                                                                                    ggCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCGTGCTGCGTGTGCTGCAGGAAGGCgagaga                                                                                                         >  1:527946/1‑151 (MQ=255)                                                                                                                                                                                                           aaaaaGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGACCTGAAAAACCTGGCCAAggcc                  <  2:449478/233‑1 (MQ=255)                                                                                                                                                                                                              aaGGCGCGTTCACCGGCGCtggcgccggtgaacgcgcccctttcgtggccgaacagttcggattcgatcagcgtttcggggat                                                                                                                                                                     >  2:506405‑M1/1‑19 (MQ=255)                                                                                                                                                                                                                        cACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTc                                                                                  <  2:246439/156‑1 (MQ=255)                                                                                                                                                                                                                        cACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAACGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGa                                        >  2:680468/1‑198 (MQ=255)                                                                                                                                                                                                                         aCCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGCGATACGCCGGGTAGGTTCGGTGCAGCCGc                                                                                >  2:6381/1‑157 (MQ=255)                                                                                                                                                                                                                         aCCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGACCTGAAAAACCTGGCCAAGGCCGGCCAGTTCCGTGAAg  >  1:280765/1‑235 (MQ=255)                                                                                                                                                                                                                           cGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCg                                                                                                                                        <  2:150730/99‑1 (MQ=255)                                                                                                                                                                                                                            ggCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTGCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCGGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCg                                                                                          <  2:47021/144‑1 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                                                                    CCCATGCAGGACATGTACAGCAAGATCCGCAAGGTCGCGCCTACCGACTCCAATGTGCTGATCCAGGGCGAGTCGGGCACCGGTAAAGAGCTGGTGGCCCGCGCCCTGCACAACCTGTCTCGCCGGGCCAAGGCACCGATGATCTCGGTGAACTGCGCGGCCATCCCCGAAACGCTGATCGAATCCGAACTGTTCGGCCACGAAAAAGGCGCGTTCACCGGCGCCAGCGCCGGGCGCGCCGGCTTGGTGGAGGCCGCCGATGGCGGTACGCTGTTCCTCGATGAAATTGGCGAACTGCCGCTCGAAGCCCAGGCTCGCCTGCTGCGTGTGCTGCAGGAAGGCGAGATACGCCGGGTAGGTTCGGTGCAGTCGCAAAAGGTCGATGTGCGCCTGATCGCCGCGACCCACCGCGACCTGAAAAACCTGGCCAAGGCCGGCCAGTTCCGTGAAG  >  AE015451/5337022‑5337472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.