New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5545666	NA (NA)	32 (0.520)	30/272	1.7	55.7%	intergenic (‑806/+71)	rpsF/rlmB	30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
	?	NC_002947	5621244 =	26 (0.410)					coding (20/774 nt)	PP_4939	hypothetical protein

AACCATAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGAC  >  NC_002947/5545528‑5545814                                                                                                                                            |                                                                                                                                                      aaCCATAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAgg                                                                                                                                             <  7:143712/149‑1 (MQ=34)     aTAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGaa                                                                                                                                         <  2:58064/149‑1 (MQ=38)          aaaGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCaa                                                                                                                                    >  4:86036/1‑149 (MQ=255)                    gcggcTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTa                                                                                                                         <  6:17672/149‑1 (MQ=255)                     cggcTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCATTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAg                                                                                                                        <  7:125508/149‑1 (MQ=255)                     cggcTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAg                                                                                                                        <  2:256912/149‑1 (MQ=255)                               aCCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGt                                                                                                                          <  1:300248/137‑1 (MQ=255)                               aCCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGt                                                                                                                          >  2:300248/1‑137 (MQ=255)                                            ggCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAgg                                                                                                 <  2:340446/149‑1 (MQ=255)                                                aaTGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                              >  6:75497/1‑148 (MQ=255)                                                  tGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGTAGCGGGTTCTCACGCGAAGAGGCCGGa                                                                                            >  5:103238/1‑148 (MQ=255)                                                  tGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGaa                                                                                           <  5:75497/149‑1 (MQ=255)                                                          tAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCt                                                                                     >  8:17504/1‑147 (MQ=255)                                                                  gATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAAt                                                                                                                                   >  4:125582/1‑94 (MQ=255)                                                                  gATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCa                                                                             <  2:37539/147‑1 (MQ=255)                                                                        aGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGa                                                                     >  6:285563/1‑149 (MQ=255)                                                                        aGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGa                                                                     >  2:105124/1‑149 (MQ=255)                                                                         gTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGAc                                                                    <  3:86036/149‑1 (MQ=255)                                                                             aGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGTACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTg                                                                 >  1:245021/1‑149 (MQ=255)                                                                             aGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGc                                                                >  4:4642/1‑149 (MQ=255)                                                                                         attcgcATACTGTTTGCTGTGCG‑ACAGGGCATCCCGTAAGTGCTGGTTGATCTCCTACAGGGGAACGAAATCACCC‑TGTAGGAGCGGGTTCACGCGCGAAGAGTCCGGAACAGGCTTATAGTCAGCGCTTTACCTGCCGCTGACGCAc                                                     <  6:103238/145‑1 (MQ=255)                                                                                         aTGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGc                                                                <  3:325068/137‑1 (MQ=255)                                                                                         aTGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGc                                                                >  4:325068/1‑137 (MQ=255)                                                                                         aTGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACg                                                    >  6:162661/1‑149 (MQ=255)                                                                                          tGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAAc                                                                                          >  4:75604/1‑110 (MQ=255)                                                                                          tGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAAc                                                                                          <  3:75604/110‑1 (MQ=255)                                                                                            cgcATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGc                                                  <  5:285563/148‑1 (MQ=255)                                                                                                     tttGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAg                                         <  2:307553/148‑1 (MQ=255)                                                                                                        gCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACa                                      >  1:99662/1‑148 (MQ=255)                                                                                                             gCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAAcccc                                >  6:4964/1‑149 (MQ=255)                                                                                                              cG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTga                                                                                   >  4:173265/1‑97 (MQ=255)                                                                                                              cG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTga                                                                                   <  3:173265/97‑1 (MQ=255)                                                                                                              cG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCg                               >  5:89786/1‑149 (MQ=255)                                                                                                                 aCAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGt                             <  3:4642/149‑1 (MQ=255)                                                                                                                  cAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTc                            <  7:17504/149‑1 (MQ=255)                                                                                                                  cAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTc                            <  5:4964/149‑1 (MQ=255)                                                                                                                  cAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTc                            <  6:270713/149‑1 (MQ=255)                                                                                                                   aGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCAAGTAGGAGCGGGTTCACCCGCGAAGCGGCCGGAACAGCCTGAGAGTCAGCGCTTGACCTGACGCTGACGCACGGCTTCGAACAGAAAAACCCCGGTc                            >  1:92405/1‑149 (MQ=38)                                                                                                                     cgcAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGc                          >  5:353321/1‑148 (MQ=255)                                                                                                                           ccGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGac                   >  8:263340/1‑149 (MQ=255)                                                                                                                            cGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                       >  3:48043/1‑144 (MQ=255)                                                                                                                            cGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                       <  4:48043/144‑1 (MQ=255)                                                                                                                              gAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACg                >  3:207278/1‑149 (MQ=255)                                                                                                                                   gCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAg           <  2:99662/149‑1 (MQ=255)                                                                                                                                   gCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAg           <  5:162661/149‑1 (MQ=255)                                                                                                                                    cTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAgg          <  2:245021/149‑1 (MQ=255)                                                                                                                                       ggTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGgctg       >  5:65849/1‑149 (MQ=255)                                                                                                                                        gTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGgctgc      >  6:48883/1‑149 (MQ=255)                                                                                                                                        gTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGgctgc      <  5:48883/149‑1 (MQ=255)                                                                                                                                            tctcCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGAc  >  7:34999/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                      AACCATAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCG‑ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCC‑TGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGAC  >  NC_002947/5545528‑5545814

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.