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

AGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATGCACCCCGCC  >  NC_002947/5531404‑5531694                                                                                                                                                   |                                                                                                                                                 aGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAgg                                                                                                                                                >  5:270497‑M2/1‑147 (MQ=255) aGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAgg                                                                                                                                                <  8:101130‑M2/149‑3 (MQ=255)    aCTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGGACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgc                                                                                                                                             >  7:101130‑M2/1‑144 (MQ=255)      tGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccg                                                                                                                                           <  4:171790‑M2/149‑8 (MQ=255)                   aTGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGTCGTTggg                                                                                                                              >  2:231051/1‑149 (MQ=255)                           cACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCgg                                                                                                                      >  7:202385/1‑149 (MQ=255)                             ccGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGGAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCg                                                                                                                       >  5:143498/1‑146 (MQ=255)                             ccGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGGAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCg                                                                                                                       <  6:143498/146‑1 (MQ=255)                                cgTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGGGAAc                                                                                                                 >  5:7307/1‑149 (MQ=255)                                 gTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCAt                                                                                                                                       <  5:266417/126‑1 (MQ=255)                                 gTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCAt                                                                                                                                       >  6:266417/1‑126 (MQ=255)                                   aGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGa                                                                                                               >  3:255658/1‑148 (MQ=255)                                    gATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATa                                                                                                             <  5:243889/149‑1 (MQ=255)                                      tGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAAc                                                                                                                 <  2:157606/143‑1 (MQ=255)                                      tGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAAc                                                                                                                 >  1:157606/1‑143 (MQ=255)                                          cacGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAgt                                                                                                       >  4:26522/1‑149 (MQ=255)                                             gAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGcc                                                                                                                                    >  4:67294/1‑117 (MQ=255)                                             gAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGcc                                                                                                                                    <  3:67294/117‑1 (MQ=255)                                                cTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCa                                                                                                 <  4:255658/149‑1 (MQ=255)                                                   gAGGCTGGCGTTCTACTCGAAGCCGAAGAACTCGTGGATAGGAACACCGCCATCCTTGCCCCGCCGGCAGAAATCAAGGCCGTAGATGGTGGGTGAAGGTTACGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCa                                                                                              >  8:218462/1‑149 (MQ=255)                                                    aGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCAc                                                                                             >  7:9346/1‑149 (MQ=255)                                                            gTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGaa                                                                                     <  3:171790/149‑1 (MQ=255)                                                                tACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAt                                                                                 <  6:63222/149‑1 (MQ=255)                                                                 aCTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtc                                                                                >  1:154050/1‑149 (MQ=255)                                                                   tCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtctc                                                                              >  7:76883/1‑149 (MQ=255)                                                                     gAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGAtctc                                                                              <  6:7307/147‑1 (MQ=255)                                                                     gAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGc                                                                            >  6:202491/1‑149 (MQ=255)                                                                     gAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGc                                                                            >  6:62878/1‑149 (MQ=255)                                                                       aGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCa                                                                          <  5:202491/149‑1 (MQ=255)                                                                            aagaaCTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGcc                                                                     <  5:62878/149‑1 (MQ=255)                                                                                 cTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGTGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcatcaagttcgtgttcatctacgcggtgctgttcatgttc                                                                <  8:177276‑M2/149‑83 (MQ=255)                                                                                  tCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGt                                                               >  3:136521/1‑149 (MQ=255)                                                                                    gTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCa                                                             >  2:100223/1‑149 (MQ=255)                                                                                        aTCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctgg                                                         >  3:63744‑M2/1‑60 (MQ=255)                                                                                        aTCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAggtgccgatccacgagttcttcggcttcgagtacaacgccagcctcaagttcgtgttcatctacgcggtgctgttcatggtcgtgctg                                                          <  4:63744‑M2/148‑89 (MQ=255)                                                                                            gCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGc                                                      >  6:221979/1‑148 (MQ=255)                                                                                                             gCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCAt                                    <  1:100223/149‑1 (MQ=255)                                                                                                                  gcggcCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATgcgc                                >  3:219651/1‑148 (MQ=255)                                                                                                                         aaCTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCTCAACACCgg                        >  8:78052/1‑149 (MQ=255)                                                                                                                          aCTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCgg                        <  4:219651/148‑1 (MQ=255)                                                                                                                              aaGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGc                   <  8:9346/149‑1 (MQ=255)                                                                                                                               aGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGcc                  >  7:45351/1‑149 (MQ=255)                                                                                                                                   cgtagaagGTGGGTTAAGGTGCCGGCATGCCGTTGGGGCCACCGGGGAACGATAGCCAGTTGATCAGCACCACGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAgg              <  7:218462/146‑1 (MQ=38)                                                                                                                                   cGAAGAAGGTGGGTGAAGGTGCCGGCATGTCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAgg              <  1:231051/149‑1 (MQ=255)                                                                                                                                   cGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAg               >  1:115479/1‑148 (MQ=255)                                                                                                                                    gaagaaGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGa             <  2:154050/149‑1 (MQ=255)                                                                                                                                      agaagGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATg           <  3:26522/149‑1 (MQ=255)                                                                                                                                            tgggtgAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATGCAcccc     <  8:202385/149‑1 (MQ=255)                                                                                                                                             gggtgAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATGCACCCCg    >  2:140871/1‑149 (MQ=255)                                                                                                                                              ggtgAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATgcgc                                >  2:70410/1‑120 (MQ=255)                                                                                                                                               gtgAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATGCACCCCGcc  <  4:136521/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                 AGCACTGCCAGCACGACCATGAACAGCACCGCGTAGATGAACACGAACTTGAGGCTGGCGTTGTACTCGAAGCCGAAGAACTCGTGGATCGGCACCCCGCCATCCTTGGCCCGGCGGCCGAACTCAAGGCCGAAGAAGGTGGGTGAAGGTGCCGGCATGCCGTTGGGGCCACCGGTGAACGATAGCCAGTTGTTCAGCACCAGGCGAATGATCTCGCCAAAGCCCAGCGTCACGATCGCCAGGTAGTCACCGTGCATGCGCAACACCGGGAAGCCGAGGATGCACCCCGCC  >  NC_002947/5531404‑5531694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ 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.