New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4150085	59 (0.810)	12 (0.190)	10/212	NT	17.9%	intergenic (+40/‑357)	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
	?	NC_002947	= 4150116	60 (0.960)					intergenic (+71/‑326)	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein

GCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4149920‑4150085 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttcgcgggtaaacccgcTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAATAC  <  NC_002947/4150116‑4149969                                                                                                                                                                                                                                                                                                                             GCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCT                                                                                                                                                                       >  2:629007/1‑150  CCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACTAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTT                                                                                                                                                                      >  2:265482/1‑150             CCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAAC                                                                                                                                                           >  1:921581/1‑150                             TGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGG                                                                                                                                           >  1:1408376/1‑150                               TATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTGCGACGGGCT                                                                                                                                         >  2:781111/1‑150                                              ACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTG                                                                                                                             >  2:697305/1‑147                                              ACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTG                                                                                                                             <  1:697305/147‑1                                                    ATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGG                                                                                                                    <  1:781111/150‑1                                                     TTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGG                                                                                                                   >  1:1225939/1‑150                                                     TTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGG                                                                                                                   <  2:1408376/150‑1                                                     TTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGG                                                                                                                   <  2:1225939/150‑1                                                                                                                    TCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCG                                                                                                                     >  1:1116516/1‑85                                                                                                                    TCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCG                                                                                                                     <  2:1116516/85‑1                                                                                                                      CCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGG                                                                                                                    >  1:1212849/1‑84                                                                                                                      CCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGG                                                                                                                    <  2:1212849/84‑1                                                                                                                                                      TTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCT                                                                             >  2:41962/1‑90                                                                                                                                                      TTCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCT                                                                             <  1:41962/90‑1                                                                                                                                                       TCGCGGGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTCCCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTT                <  1:901560/150‑1                                                                                                                                                         GCGGGTAAGCCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCA              <  2:743439/150‑1                                                                                                                                                           ggtTAAACCCGCGCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACA            <  2:802774/147‑1                                                                                                                                                            GGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTC                              >  1:1282758/1‑131                                                                                                                                                            GGTAAACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTC                              <  2:1282758/131‑1                                                                                                                                                              TAAACCCGCCTCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTG         <  1:1652558/150‑1                                                                                                                                                                 ACCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGA      <  1:1335493/150‑1                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAA     <  2:553337/150‑1                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATT          <  2:1597340/145‑1                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATT          >  1:1597340/1‑145                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCT                                            >  2:1751085/1‑111                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCT                                            <  1:1751085/111‑1                                                                                                                                                                  CCCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCC‑CGCTGTGGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAA     >  1:1505714/1‑150                                                                                                                                                                   CCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAAT    >  1:129667/1‑150                                                                                                                                                                   CCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑AGGCCGG                                                                                              >  2:1631552/1‑60                                                                                                                                                                   CCGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑AGGCCGG                                                                                              <  1:1631552/60‑1                                                                                                                                                                   CCGATCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCCACCGATCCTGGCTCCCTTCCTTCATCACCAAAGTCGACCTCAAGCGTTTCACATTGGGAct    >  2:1558394/1‑148                                                                                                                                                                    CGCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCGTCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAATA   <  2:781972/150‑1                                                                                                                                                                     GCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAATAC  <  1:1668117/150‑1                                                                                                                                                                     GCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAG                                 >  2:195753/1‑119                                                                                                                                                                     GCTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAG                                 <  1:195753/119‑1                                                                                                                                                                                                                                                                                                                             GCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4149920‑4150085 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttcgcgggtaaacccgcTCCTGCGACGGGCTACGTCACCTTTGCAGGCGCGGGTTTACCCGCGAAG‑GGGCCGGCACAAGAGGAAACAGCTACATGGGGAGCAACCGATCCTGGATCACTTCCTTCATCACCAAGGTCGAGCTCAAGCGTTTCACATTGGGAATAC  <  NC_002947/4150116‑4149969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.