New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 652785	44 (0.840)	32 (0.730)	21/206	NT	63.5%	coding (1961/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4808204	0 (0.000)					intergenic (‑268/‑287)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2

GCCAGCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652629‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATACACACCGCGACACATTG  <  NC_002947/4808204‑4808057                                                                                                                                                                                                                                                                                                                   GCCAGCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCT                                                                                                                                                             >  2:206590/1‑150   CAGCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGGGGGGCTCG                                                                                                                                                           >  1:267824/1‑150       AGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCCCGCGCGGCGCTtcgcgg                                                                                                                                                       <  2:838442/150‑7                                                                            aaatccCGCCGGAATAATGGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAG                                                                                  >  2:770561/7‑150                                                                             aatccCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGG                                                                                 <  2:857162/145‑1                                                                                 cCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCT                                                                             >  2:858663/2‑150                                                                                  CGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGCACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTG                                                                            >  1:84380/1‑150                                                                                  CGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTG                                                                            >  2:1283902/1‑150                                                                                      GGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAA                                                                        <  1:740956/150‑1                                                                                       GAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAAC                                                                       >  1:1222518/1‑150                                                                                             TTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCG                                                                 >  2:637439/1‑150                                                                                             TTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCG                                                                 >  1:307043/1‑150                                                                                                 CCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAA                                                             >  2:971324/1‑150                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAA                                                            <  2:1296074/150‑1                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAA                                                            >  2:815505/1‑150                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGA                                                                                                           >  2:142924/1‑103                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGA                                                                                                           <  1:142924/103‑1                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAA                                                                                                                                         >  2:1001567/1‑73                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAA                                                                                                                                         <  1:1001413/73‑1                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAA                                                                                                                                         >  2:1001413/1‑73                                                                                                  CCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAA                                                                                                                                         <  1:1001567/73‑1                                                                                                   CGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAAC                                                           >  2:555548/1‑150                                                                                                         AAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTAC                                                     >  1:1395462/1‑150                                                                                                         AAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTAC                                                     <  1:637439/150‑1                                                                                                            CGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGACCACCTCCCAGGCGCTGAAAATCCCCCGGCGAAAACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCG                                                  >  1:455134/1‑150                                                                                                             GTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACGTTCTAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGC                                                 >  1:1380681/1‑150                                                                                                              TAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCC                                                <  2:1222518/150‑1                                                                                                                     GGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGACCGCCTTCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGC                                         <  1:246615/150‑1                                                                                                                     GGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGC                                         <  2:1390952/150‑1                                                                                                                        TTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCTAACACCTCCCAGGCGCTGAAACTCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAA                                      <  2:18294/150‑1                                                                                                                             CCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCG                                 >  1:208802/1‑150                                                                                                                             CCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCG                                 >  1:442242/1‑150                                                                                                                             CCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCG                                 >  2:669447/1‑150                                                                                                                               GCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCC                               <  1:770561/150‑1                                                                                                                                   AGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATT                           >  1:315200/1‑150                                                                                                                                      GCCGCGCGGGCGTCTCTCGATCTCCCAGGCTCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAGATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCC                        <  2:442242/150‑1                                                                                                                                      GCCGCACGGGCGGCGCTCGATCGCCGACGCGCGAAATCTCTCCCGGCGAACCCCTCCCAGGCACTGAAAATCCCCCGGCGAACACCTCCCAGGCGCGGAAAACCCCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCC                        <  2:1394104/150‑1                                                                                                                                         GCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTA                     <  2:84380/150‑1                                                                                                                                          CGCGGGCGGCGCTCGCTCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCCGGCGCTGAAAAC                                                                       <  2:20034/99‑1                                                                                                                                          CGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAAC                                                                       >  1:20034/1‑99                                                                                                                                           GCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATA                   <  1:669447/150‑1                                                                                                                                           GCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATA                   <  1:971324/150‑1                                                                                                                                                 GGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTGTACACACC             <  2:1380681/150‑1                                                                                                                                                 GGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCCCCAAAGCGCGAATTCCTCCCATTGCCCTATACACACC             >  2:1083667/1‑150                                                                                                                                                     CTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCATGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATACACACCGCGA         <  1:363902/150‑1                                                                                                                                                     CTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGC                                                 <  1:295241/110‑1                                                                                                                                                     CTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGC                                                 >  2:295241/1‑110                                                                                                                                                            TCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATACACACCGCGACACATTG  >  1:931934/1‑150                                                                                                                                                                                                                                                                                                                   GCCAGCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652629‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATACACACCGCGACACATTG  <  NC_002947/4808204‑4808057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.