New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4593859	29 (0.500)	3 (0.060)	3/294	NT	9.5%	intergenic (+165/+134)	mccA/PP_4068	methylcrotonyl‑CoA carboxylase biotin‑containing subunit alpha/Transcriptional regulator, Cro/CI family
	?	AE015451	= 4593904	32 (0.650)					intergenic (+210/+89)	mccA/PP_4068	methylcrotonyl‑CoA carboxylase biotin‑containing subunit alpha/Transcriptional regulator, Cro/CI family

GGCCGCTTTGCGGCCCTAACGCAACACAAGGCCGCCCCTGCAACAGCCCGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGCTGCCCACCTTCCTCGGCCAGCTCGCGGAAAATCG  >  AE015451/4593706‑4594126                                                                                                                                                                                                       |                                                                                                                                                                                                                               ggCCGCTTTGCGGCCCTAACGCAACACAAGGCCGCCCCTGCAACAGCCCGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgt                                                                                                                                                                                                                             <  1:135957‑M2/202‑4 (MQ=255)                      cAACACAAGGCCGCCCCTGCAACAGCCCGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACccgcc                                                                                                                                                                       <  1:942906/235‑1 (MQ=255)                                                 cGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCctgct                                                                                                                                                                                         >  2:564836/1‑190 (MQ=255)                                                   tAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTgg                                                                                                                                                                                       >  2:609062/1‑190 (MQ=255)                                                            gTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACCTCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGggccggcc                                                                                                                                                                                              >  2:936895/1‑174 (MQ=255)                                                              ttACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCCCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgc                                                                                                                                                                                                                             <  2:760436‑M2/141‑4 (MQ=255)                                                                    gcgAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcggg                                                                                                                                                                                                                    <  1:809825‑M2/144‑13 (MQ=255)                                                                         aGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACtgc                                                                                                                                                                               >  2:612272/1‑174 (MQ=255)                                                                              cgggccTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcgggtttac                                                                                                                                                                                                               <  2:645115‑M2/139‑18 (MQ=255)                                                                                   ctgctgGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTACACacgc                                                                                                                                                                        >  1:565770/1‑173 (MQ=255)                                                                                         gCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcgggtttacccg                                                                                                                                                                                                            <  2:1013723‑M2/131‑21 (MQ=255)                                                                                                 ctACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGTTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCagcga                                                                                                                                                                                                                               >  2:130509/1‑103 (MQ=255)                                                                                                   aCCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGa                                                                                                              >  1:402027/1‑215 (MQ=255)                                                                                                      cGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGaaa                                                                                                 >  2:693094/1‑225 (MQ=255)                                                                                                      cGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGGAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtg                                                                                                                                                                                                                              <  2:142669‑M2/100‑3 (MQ=255)                                                                                                        tCGCTGACCGTTGCCGCCGCTACAGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGccc                                                                                                                                                                                             <  2:518888/131‑1 (MQ=255)                                                                                                             cACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCac                                                                                                                                                     >  1:1088183/1‑166 (MQ=255)                                                                                                                        ccgcTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGaaa                                                                                                 >  1:794244/1‑207 (MQ=255)                                                                                                                                 tATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcgggtttacccgcgaatacggtagcggcggcaacggtgagcgacg                                                                                                                                                                           >  1:370723‑M2/1‑71 (MQ=255)                                                                                                                                      gcgGGTAAACCCGCTGCTACAGCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGc                                                                                            <  2:920275/198‑1 (MQ=255)                                                                                                                                      gcgGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCTGGTAGTTACTGtt                                                       <  1:564839/235‑1 (MQ=255)                                                                                                                                      gcgGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGtt                                                       <  1:609065/235‑1 (MQ=255)                                                                                                                                                ccGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcgggtttacccgcgaatacggtagcggcggcaacggtga                                                                                                                                                                                 >  1:814047‑M2/1‑56 (MQ=255)                                                                                                                                                ccGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGtgtaggagcgggtttacccgcgaatacggtagcggcggcaacggtga                                                                                                                                                                                 <  2:814044‑M2/103‑48 (MQ=255)                                                                                                                                                ccGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCAc                                                                                                                <  2:489129/168‑1 (MQ=255)                                                                                                                                                     ccTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGccc                                                                                                                      >  1:162010/1‑155 (MQ=255)                                                                                                                                                       tACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCg                                                                    >  1:1073216/1‑205 (MQ=255)                                                                                                                                                       tACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCACTGCCTTCAGATAACg                                     >  1:226592/1‑236 (MQ=255)                                                                                                                                                         cATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTc                                                                                              <  2:990773/177‑1 (MQ=255)                                                                                                                                                         cATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGc                                                                                            <  1:959549/179‑1 (MQ=255)                                                                                                                                                           tCCGACCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCcgcg                                                                                                                                                                                                                                <  2:706339/45‑1 (MQ=255)                                                                                                                                                                   ggggTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGTTGCCCACCTTc                         >  1:791552/1‑236 (MQ=255)                                                                                                                                                                           cacaTGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCa                                                                                                                 <  1:685268/140‑1 (MQ=255)                                                                                                                                                                           cacaTGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCa                                                                                                                 >  2:685265/1‑140 (MQ=255)                                                                                                                                                                                 ttGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCacaaca                                                                          >  2:382945/1‑173 (MQ=255)                                                                                                                                                                                         tAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGCTGCCCACCTTCCTCGGCCAGCTCGCGGAAAAt    >  1:949253/1‑235 (MQ=255)                                                                                                                                                                                          aGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCa                                                                                                                           <  2:402024/115‑1 (MQ=255)                                                                                                                                                                                           ggCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACg                                     >  2:312156/1‑200 (MQ=255)                                                                                                                                                                                           ggCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGCTGccccc                             >  2:318058/1‑206 (MQ=255)                                                                                                                                                                                            gcgcAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACACCAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGCTGCCCACCTTCCTCGGCCAGCTCGCGGAAAATCg  >  2:388623/1‑234 (MQ=255)                                                                                                                                                                                             cgcAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTgccg                                                                                                                                                         >  1:373062/1‑82 (MQ=255)                                                                                                                                                                                             cgcAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTgccg                                                                                                                                                         <  2:373059/82‑1 (MQ=255)                                                                                                                                                                                                 ggCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAAc                                                                                         <  2:991746/142‑1 (MQ=255)                                                                                                                                                                                                      ggtgtaggagcgggtttgcccgcgaatacggtagcggcggcaacggtgagcgacgggtagagattggccagcaggcccggccctttcgcgggtaaacccgctcctacgggctgttgcag                                                                                                           >  2:233905‑M2/2‑2 (MQ=255)                                                                                                                                                                                                       |                                                                                                                                                                                                                               GGCCGCTTTGCGGCCCTAACGCAACACAAGGCCGCCCCTGCAACAGCCCGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCTACCCGTCGCTCACCGTTGCCGCCGCTACCGTATTCGCGGGTAAACCCGCTCCTACATCCGATCGGGGGTGGACACATGTTGGTGATTAGGCGCAGGCCGCGTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGCCCTGCTGGCCAACTTCCACCCGCCGTTCACCGTTGCCGCCACTACTCAAACCCTTTCAAAAAGCCCCATGCACCCGCACGACCACCCCAAGAAATTCGCAACCCTCTTCGCACAACAGCGCCGGGTAGTTACTGTTCAATGCCTTCAGATAACGCTGCCCACCTTCCTCGGCCAGCTCGCGGAAAATCG  >  AE015451/4593706‑4594126

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.