New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5344519 =	50 (1.150)	12 (0.350) +TAGGAGCGGGTTTACCCGCGAAGAGGCCG	11/208	2.3	27.5%	intergenic (+46/‑132)	pgi‑II/acsA‑II	glucose 6‑phosphate isomerase/acetyl‑CoA synthetase
	?	NC_002947	= 5506607	31 (0.710)					intergenic (+18/‑181)	PP_4839/cycA	iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease

CTGGAAGGCGGCAGTGGCCGTGATGCTGGTGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAATGCAGAGTCGATCTGTCGCGCCCCGATCTGGAACGCGCGTGTTAGC  >  NC_002947/5506460‑5506752                                                                                                                                                    |                                                                                                                                                  ttGGAAGGGTGCAGTGGCCGTGATGTTGGGGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGGTGGTGGTGATGAGGTGGGTGGATTTTTTGGTTTTACGTCACCGCCGGGTCTTTGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTg                                                                                                                                                 <  1:20535/149‑1 (MQ=255) cctgatggcggcAGTGGTCGTGATGCTGGTGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTg                                                                                                                                                 <  1:431450/144‑1 (MQ=255)           gcAGTGGCCGTGATGCTGGTGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTcgc                                                                                                                                       <  1:678315/150‑1 (MQ=255)                    gTGATGCTGGTGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGACCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAAcc                                                                                                                              <  2:624240/150‑1 (MQ=255)                           tggtgctggGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCt                                                                                                                       >  1:325083/1‑150 (MQ=255)                              tgctggGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACg                                                                                                                    >  1:292179/1‑150 (MQ=255)                                   ggggTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGa                                                                                                               >  2:713076/1‑150 (MQ=255)                                          tGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGGGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGtt                                                                                                        <  1:713076/150‑1 (MQ=255)                                            ttCCCGCTGGTGGCGGTGTTGATGGTTGTGATTTTGTGGGTGGATAGTTTGGTGGTGCGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCtggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgt                                                                                                      >  1:666467‑M2/1‑105 (MQ=255)                                             tCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTACcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgta                                                                                                     >  2:661414‑M2/1‑104 (MQ=255)                                                   tggtggGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCg                                                                                               <  2:460952/150‑1 (MQ=255)                                                      ggggggTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGt                                                                                            <  1:1043628/149‑1 (MQ=255)                                                              tCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGACCGCGTTGTAGGAGCGGGTTTACCcgc                                                                                    <  1:524160/150‑1 (MQ=255)                                                                gATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGa                                                                                  >  2:897042/1‑150 (MQ=255)                                                                        tgATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCtggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgggtt                                                                                           <  2:209842‑M2/133‑57 (MQ=255)                                                                        tgATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCtggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgggtt                                                                                           >  1:209842‑M2/1‑77 (MQ=255)                                                                                   gTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGtt                                                                                                        >  2:72170/1‑109 (MQ=255)                                                                                   gTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGtt                                                                                                        <  1:72170/109‑1 (MQ=255)                                                                                    tGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTACcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtagga                                                                                                  >  1:631355‑M2/1‑65 (MQ=255)                                                                                    tGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTACcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtagga                                                                                                  <  2:631355‑M2/114‑50 (MQ=255)                                                                                      gATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATg                                                            >  1:757478/1‑150 (MQ=255)                                                                                       aTAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgg                                                                                              <  2:166471‑M2/115‑54 (MQ=255)                                                                                       aTAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgg                                                                                              >  1:166471‑M2/1‑62 (MQ=255)                                                                                       aTAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGc                                                           <  1:1014186/150‑1 (MQ=255)                                                                                          gtgtggtggTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTCCCCGCGAAGAGGCCGGTACAGGCGAAATGCTGa                                                        <  2:542268/147‑1 (MQ=255)                                                                                           tttGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCtggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtag                                                                                                    <  2:868989‑M2/105‑48 (MQ=255)                                                                                           tttGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCtggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtag                                                                                                    >  1:868989‑M2/1‑58 (MQ=255)                                                                                               gtggtgAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGa                                                   >  2:201296/1‑150 (MQ=255)                                                                                                   tgAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAAt                                               <  2:372219/150‑1 (MQ=255)                                                                                                    gAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCt                                                          <  1:44802/138‑1 (MQ=255)                                                                                                    gAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCt                                                          >  2:44802/1‑138 (MQ=255)                                                                                                                   cTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAATGCAGAGTCGATCTGTc                               <  2:325083/150‑1 (MQ=255)                                                                                                                    ttGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAg                                                       <  2:39307/125‑1 (MQ=255)                                                                                                                    ttGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAg                                                       >  1:39307/1‑125 (MQ=255)                                                                                                                         cAGCGCTTGAGCCTTGTGTTGCCTGTACcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgg                                                                                              <  2:598971‑M2/81‑54 (MQ=255)                                                                                                                         cAGCGCTTGAGCCTTGTGTTGCCTGTACcggcctcttcgcgggtaaacccgctcctacaacgcggtccctcgtaggagcgg                                                                                              >  1:598971‑M2/1‑28 (MQ=255)                                                                                                                          aGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGa                                                        <  2:682275/118‑1 (MQ=255)                                                                                                                          aGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGa                                                        >  1:682275/1‑118 (MQ=255)                                                                                                                               ttGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACAGGGGAACGCGTTGTAGCAGAGGGTTCACACGCGAAGAGGCCGGGAAAGGGGAAATGCTGAGCTGAAGATTTAGAGGGTAACTGTCACGCTCCGATCt                   >  2:224947/1‑150 (MQ=16)                                                                                                                                      ttGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGa                                                        <  1:314351/106‑1 (MQ=255)                                                                                                                                      ttGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGa                                                        >  2:314351/1‑106 (MQ=255)                                                                                                                                        gtgtTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAATGCAGAGTCGATCTGTCGCGCCCCGATCTGGAAcgcgc          <  2:292179/150‑1 (MQ=255)                                                                                                                                                tgtgCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAATGCAGAGTCGATCTGTCGCGCCCCGATCTGGAACGCGCGTGTtagc  >  1:35724/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CTGGAAGGCGGCAGTGGCCGTGATGCTGGTGCTGGGGGTGATGTTCCCGCTGGTGGGGGTGTCGATGGTGGTGATGTGGGGGGTGGATAGTTTGGTGGTGAGGCGCCGCCGGGTCTTGGCCAGCGCTTGAGCCTTGTGTTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCGCGTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACAGGCGAAATGCTGAGCCGAAAATGCAGAGTCGATCTGTCGCGCCCCGATCTGGAACGCGCGTGTTAGC  >  NC_002947/5506460‑5506752

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.