New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4266523 =	43 (1.020)	4 (0.100)	4/244	NT	9.1%	intergenic (‑65/+81)	PP_3738/galP‑IV	transcriptional regulator VanR/porin‑like protein
	?	NC_002947	4266610 =	39 (0.980)					coding (1248/1254 nt)	galP‑IV	porin‑like protein

GGCGACTTCCAAAGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCACCTCGGCATCGCGCTCCCA  >  NC_002947/4266462‑4266753                                                                                                                                                     |                                                                                                                                                 ggCTACTTACAAAGACATGAGCGGCCATCTAAGCTCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGACCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAg                                                                                                                                                  <  8:52460/149‑1 (MQ=37)       ttCCAAAGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGc                                                                                                                                            >  1:203571/1‑149 (MQ=255)       ttCCAAAGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGc                                                                                                                                            >  8:72772/1‑149 (MQ=255)       ttCCAAAGACATGAGCGGGCAACATAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGCTGAACCCGCCCCTACAAgagatcg                                                                                                                                            >  5:206629/1‑143 (MQ=37)           aaaGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGa                                                                                                                                         >  5:129094/1‑148 (MQ=255)             aGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGACTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAg                                                                                                                                      >  8:225380/1‑149 (MQ=255)                 aTGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGa                                                                                                                                  <  2:203571/149‑1 (MQ=255)                 aTGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGa                                                                                                                                  <  3:13688/149‑1 (MQ=255)                   gAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGAc                                                                                                                                 >  1:132912/1‑148 (MQ=255)                       gggCATCTTAGCGAAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCa                                                                                                                            <  1:140650/149‑1 (MQ=255)                        ggCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAg                                                                                                                           <  4:89015/149‑1 (MQ=255)                        ggCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAg                                                                                                                           >  6:27249/1‑149 (MQ=255)                        gccATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAg                                                                                                                           <  5:103670/147‑1 (MQ=255)                               tAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTc                                                                                                                    >  5:241820/1‑149 (MQ=255)                                    cAAGCGGAGGGGTTGCTGCAGGCGTGTTGTAGGTGCGGGTTCACCCGCTAAGCAGGCAACGCGTAACTTGGCACGGGCGGCGCGGGTGTTGGCGGGTTAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTc                                                                                                               <  2:132912/149‑1 (MQ=255)                                     aaGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCg                                                                                                              <  5:27249/149‑1 (MQ=255)                                           aGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCa                                                                                                       >  4:240388/1‑149 (MQ=255)                                           aGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCa                                                                                                       <  7:139442/149‑1 (MQ=255)                                           aGGGGGTGCTGCAGGCCTGGAGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCa                                                                                                       <  5:264432/149‑1 (MQ=255)                                               gTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGAc                                                                                                                                 <  8:134802/120‑1 (MQ=255)                                               gTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGAc                                                                                                                                 >  7:134802/1‑120 (MQ=255)                                                ttGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGtt                                                                                                  <  3:240388/149‑1 (MQ=255)                                                   ctgcAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGa                                                                                                <  7:37768/148‑1 (MQ=255)                                                         gCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTgcg                                                                                         >  8:83433/1‑149 (MQ=255)                                                                 TAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGTTAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCTCTGTTGAAGCTGCGCCGGTTg                                                                                  >  7:225380‑M1/1‑148 (MQ=255)                                                                  AGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGt                                                                                <  3:62121‑M1/149‑1 (MQ=255)                                                                          gttcacccgcgaacaccggcgcagccggtgccatgttccgcgttgcctgcttcgcgggtgaacccgctcctacaaGGTCAGCGGATAGCTGATGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCgttgt                                                                        >  5:242457‑M2/76‑149 (MQ=255)                                                                          gTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCgttgt                                                                        <  7:72772/149‑1 (MQ=255)                                                                               cccgcgaacaccggcgcagccggtgccatgttccgcgttgcctgcttcgcgggtgaacccgctcctacaaGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGc                                                                   >  1:216983‑M2/71‑149 (MQ=255)                                                                                ccgcgaacaccggcgcagccggtgccatgttccgcgttgcctgcttcgcgggtgaacccgctcctacaaGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGcc                                                                  >  2:202635‑M2/70‑149 (MQ=255)                                                                                ccGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGcc                                                                  >  7:12385/1‑149 (MQ=255)                                                                                 cgcgAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCGCAGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGcc                                                                  <  1:52539/149‑1 (MQ=255)                                                                                  gcgaacaccggcgcagccggtgccatgttccgcgttgcctgcttcgcgggtgaacccgctcctacaaGGTCAGCGGATAGCTGATGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCgg                                                                <  6:242457‑M2/82‑1 (MQ=255)                                                                                       gCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGtt                                                           <  4:62121/149‑1 (MQ=255)                                                                                        cAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTg                                                          <  6:241820/149‑1 (MQ=255)                                                                                            cAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAgg                                                       >  7:23521/1‑148 (MQ=255)                                                                                                        tGGCACCGGCTGCGCCGATGTTCGCGGATGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATAACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGTTTCTTCAAAGccc                                          >  8:40023/1‑149 (MQ=255)                                                                                                         ggCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGcccc                                         >  8:232645/1‑149 (MQ=255)                                                                                                          gCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCg                                        <  7:232645/149‑1 (MQ=255)                                                                                                           cACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCg                                                                 >  4:7575/1‑123 (MQ=255)                                                                                                           cACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCg                                                                 <  3:7575/123‑1 (MQ=255)                                                                                                                  tGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGctct                                    >  3:20506/1‑145 (MQ=255)                                                                                                                  tGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGctct                                    <  4:20506/145‑1 (MQ=255)                                                                                                                      ccGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGttctt                                                  >  6:99691/1‑127 (MQ=255)                                                                                                                      ccGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGttctt                                                  <  5:99691/127‑1 (MQ=255)                                                                                                                               gcgGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCAcc                   >  4:82681/1‑149 (MQ=255)                                                                                                                               gcgGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCAc                    <  8:12385/148‑1 (MQ=255)                                                                                                                                               ctacaaGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCACCTCGGCATCGCGCTcc    >  5:83549‑M2/7‑148 (MQ=255)                                                                                                                                                  caaGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCACCTCGGCATCGCGCTCCCa  <  7:83433‑M2/144‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 GGCGACTTCCAAAGACATGAGCGGGCATCTTAGCGCAAGCCGAGGGGTTGCTGCAGGCCTGTTGTAGGAGCGGGTTCACCCGCGAAGCAGGCAACGCGGAACATGGCACCGGCTGCGCCGGTGTTCGCGGGTGAACCCGCCCCTACAAGGTCAGCGGATAGCTGACGATCAGGCGCGTCTGGTCG‑AGATCACTGTTGAAGCTGCGCCGGTTGGTCGCGTTGTTCAGCCGGATGTTGAGGTTCTTCAAAGCCCCGCTCTGGAAGGTGTAGTTCACCTCGGCATCGCGCTCCCA  >  NC_002947/4266462‑4266753

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.