New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5531499	36 (0.850)	3 (0.080)	3/244	NT	7.4%	coding (774/1308 nt)	braE	high‑affinity branched‑chain amino acid ABC transporter permease BraE
	?	NC_002947	= 5531550	41 (1.030)					coding (723/1308 nt)	braE	high‑affinity branched‑chain amino acid ABC transporter permease BraE

GCGCTTCCCAGGCCCGGCCGACCGGCATGCGAGTCAGGCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGG  >  NC_002947/5531351‑5531646                                                                                                                                                      |                                                                                                                                                    acccTTACCAGGCACGGCCCCCCGGCATGCGAGACACGCAATAAATCATGAACAGCACTCCCAGCACGACCATGAACAAAACCGAGTAGATGAACAAGAACTTCAGGCTCGCGTTGAACTAGAACCAGAAGAAATCCTGGA‑TCGGCAcc                                                                                                                                                     >  2:209698/4‑149 (MQ=255)             cccGGCCGACCGGCATGCGAGGCAGGCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTg                                                                                                                                         <  7:233657/149‑1 (MQ=255)              ccGGCCGACCGGCATGCGAGTCAGGCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTgg                                                                                                                                        <  6:97424/149‑1 (MQ=255)                     aCCGGCATGCGAGTCAGGCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCcggcg                                                                                                                                 <  5:259367/149‑1 (MQ=255)                                      gCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCg                                                                                                                 >  2:68327/1‑148 (MQ=255)                                               gATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAggt                                                                                                         <  6:21397/147‑1 (MQ=255)                                                aTGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAggtgg                                                                                                       <  1:68327/148‑1 (MQ=255)                                                aTGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAggtgg                                                                                                       <  3:49991/148‑1 (MQ=255)                                                   tACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATTAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGACACGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAggtgggtg                                                                                                    <  1:209698/149‑1 (MQ=255)                                                      aGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAgg                                                                                                <  8:101130‑M2/149‑3 (MQ=255)                                                      aGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAgg                                                                                                >  5:270497‑M2/1‑147 (MQ=255)                                                         aCTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGGACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgc                                                                                             >  7:101130‑M2/1‑144 (MQ=255)                                                           tGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccg                                                                                           <  4:171790‑M2/149‑8 (MQ=255)                                                             ccAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgat                                                                                         >  3:63744‑M1/1‑89 (MQ=255)                                                              cAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgat                                                                                         <  4:63744‑M1/148‑61 (MQ=255)                                                                    gaacatgAACAGCACCGCGTAGATGAACACGAACTTGATGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCttcacacaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgatccacgag                                                                                  <  8:177276‑M1/146‑68 (MQ=255)                                                                        aTGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGTCGTTggg                                                                              >  2:231051/1‑149 (MQ=255)                                                                                cACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCgg                                                                      >  7:202385/1‑149 (MQ=255)                                                                                  ccGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGGAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCg                                                                       <  6:143498/146‑1 (MQ=255)                                                                                  ccGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGGAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCg                                                                       >  5:143498/1‑146 (MQ=255)                                                                                     cgTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGGGAAc                                                                 >  5:7307/1‑149 (MQ=255)                                                                                      gTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCAt                                                                                       >  6:266417/1‑126 (MQ=255)                                                                                      gTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCAt                                                                                       <  5:266417/126‑1 (MQ=255)                                                                                        aGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGa                                                               >  3:255658/1‑148 (MQ=255)                                                                                         gATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATa                                                             <  5:243889/149‑1 (MQ=255)                                                                                           tGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAAc                                                                 >  1:157606/1‑143 (MQ=255)                                                                                           tGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAAc                                                                 <  2:157606/143‑1 (MQ=255)                                                                                               cacGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAgt                                                       >  4:26522/1‑149 (MQ=255)                                                                                                  gAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGcc                                                                                    >  4:67294/1‑117 (MQ=255)                                                                                                  gAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGcc                                                                                    <  3:67294/117‑1 (MQ=255)                                                                                                     cTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCa                                                 <  4:255658/149‑1 (MQ=255)                                                                                                        gAGGCTGGCGTTCTACTCGAAGCCGAAGAACTCGTGGA‑TAGGAACACCGCCATCCTTGCCCCGCCGGCAGAAATCAAGGCCGTAGATGGTGGGTGAAGGTTACGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCa                                              >  8:218462/1‑149 (MQ=255)                                                                                                         aGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCAc                                             >  7:9346/1‑149 (MQ=255)                                                                                                                 gTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGaa                                     <  3:171790/149‑1 (MQ=255)                                                                                                                     tACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAt                                 <  6:63222/149‑1 (MQ=255)                                                                                                                      aCTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtc                                >  1:154050/1‑149 (MQ=255)                                                                                                                        tCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtctc                              >  7:76883/1‑149 (MQ=255)                                                                                                                          gAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtctc                              <  6:7307/147‑1 (MQ=255)                                                                                                                          gAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGc                            >  6:202491/1‑149 (MQ=255)                                                                                                                          gAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGc                            >  6:62878/1‑149 (MQ=255)                                                                                                                            aGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCa                          <  5:202491/149‑1 (MQ=255)                                                                                                                                 aagaaCTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGcc                     <  5:62878/149‑1 (MQ=255)                                                                                                                                      cTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGTGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcatcaagttcgtgttcatctacgcggtgctgttcatgttc                <  8:177276‑M2/149‑83 (MQ=255)                                                                                                                                       tCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGt               >  3:136521/1‑149 (MQ=255)                                                                                                                                         gTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCa             >  2:100223/1‑149 (MQ=255)                                                                                                                                             a‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctgg         >  3:63744‑M2/1‑60 (MQ=255)                                                                                                                                             a‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctg          <  4:63744‑M2/148‑89 (MQ=255)                                                                                                                                                cGGCACCttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctggca       <  4:171790‑M1/149‑143 (MQ=255)                                                                                                                                                  gCACCttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgatccacgagttcttcggcttcgagtccaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctggcagt     >  7:101130‑M1/1‑5 (MQ=255)                                                                                                                                                  gCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGc      >  6:221979/1‑148 (MQ=255)                                                                                                                                                     ccttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctggcagtgct  >  5:270497‑M1/1‑2 (MQ=255)                                                                                                                                                     ccttcacccaccttcttcggccttgagttcggccgccgggccaaggatggcggggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctggcagtgct  <  8:101130‑M1/149‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GCGCTTCCCAGGCCCGGCCGACCGGCATGCGAGTCAGGCGATGCTTGATGTACAGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGA‑TCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGG  >  NC_002947/5531351‑5531646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.