New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 652785	48 (0.910)	27 (0.600)	7/224	2.1	57.0%	coding (1961/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4810126	0 (0.000)					intergenic (‑268/‑287)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2

GCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652633‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATAC  <  NC_002947/4810126‑4809995                                                                                                                                                                                                                                                                                               GCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGC                                                                                                                                                       >  1:414930/1‑136       GGAACAGCATGAAAAACAGGCGGCGCAGGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGG‑TTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:1141810/136‑1        gctCAGCTTGTAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  2:919336/133‑1        cAACCGCATGAAAACCAGCCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:1142708/135‑1        cAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGCACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:402233/135‑1        cAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:1347237/135‑1        cAACAGCATCAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:1188433/135‑1        cAACACCATCAAAACCAGGCGGCGCAGGGCGGACTCGCGAGGGGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                                <  1:478775/135‑1          ACAGCATGAAAACCAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGC                                                                                                                                              <  1:1256811/136‑1          ACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGC                                                                                                                                              >  1:908891/1‑136              CATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGAAAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGA                                                                                                                                          <  1:446322/136‑1               ATGAAAAACCGGCGGCGCTTGGCGTACTCGCGAGGTGGAACGTGCCCGGCATGATAACGCATGCGCAGGAATAATTGGCCCGAAACAACCGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGAT                                                                                                                                         <  1:1182886/136‑1               ATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGAT                                                                                                                                         >  2:26388/1‑136                gGAAAAACCGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACTAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATC                                                                                                                                        <  2:363248/135‑1                 GAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCT                                                                                                                                       >  2:1178539/1‑136                    AAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCGCGATCTaac                                                                                                                                    >  1:266564/1‑133                                                                                   GAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCTCCGGCAAACACCTCa                                                                     >  1:984390/1‑135                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCAGAAACTCTCCCCGCGAACCCCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCA                                                                   >  2:1187199/1‑136                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 <  1:829646/74‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 <  1:333520/74‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 <  1:43632/74‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 >  2:333520/1‑74                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 >  2:43632/1‑74                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                                 >  2:829646/1‑74                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAAATCCTCCGGC                                                                                                               >  2:1057251/1‑92                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAAATCCTCCGGC                                                                                                               <  1:1057251/92‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGC                                                                                                                                >  2:853800/1‑75                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGC                                                                                                                                <  1:853800/75‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                                 <  1:643370/74‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                                 >  2:1200510/1‑74                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                                 >  2:643370/1‑74                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                                 <  1:1200510/74‑1                                                                                     ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCACGCTATCCCAGGCGCTGAAACACTCCCGGCGAACACCACCCCAGCGCTGAAAAACCCCCCGCGAACACCTCCCc                                                                   >  1:990359/1‑135                                                                                                GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCc                                                                                                                                                      >  1:547169/1‑41                                                                                                GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCG                                                                                                                                                      <  2:547169/42‑1                                                                                                GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCCCGCGGGCGGCGCGCCATCTCCCAGGCGCTGGAACTCTCCCGGCGACCCCCTCCCAGGGCCTGAAAATACCCCGGCGAACACCTCCCCGGCGCTGAAAc                                                        >  2:233015/1‑135                                                                                                GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCCCCGCGCGGGCGGCGCTCGATCTACCAGGCGCTGAAACTCTACCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCCGCGAACACCACCCAGGCCCTGAAAA                                                        >  1:604338/1‑136                                                                                                 AAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAAC                                                       >  1:1006897/1‑136                                                                                                 AAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAAC                                                       >  1:600530/1‑136                                                                                                 AAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAAC                                                       >  1:362376/1‑136                                                                                                 AAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCGCCCGGCGAACCCCTCCCCGGCGCTGAAAATCCCCCGCCGAACCCCGCCCACGCCCTGcacac                                                       >  1:238008/1‑131                                                                                                    CAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAA                                                                            <  2:123890/112‑1                                                                                                    CAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAA                                                                            >  1:123890/1‑112                                                                                                               GCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGC                                                                                                                                              <  1:919598/35‑1                                                                                                               GCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGC                                                                                                                                              >  2:919598/1‑35                                                                                                                     TTACCCGCGAAGCGCCGCGCGGGCGGCACTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCC                                   >  1:947257/1‑136                                                                                                                          CGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCAACCCGCCAA                              >  1:488778/1‑136                                                                                                                                        CGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGC                <  1:598541/136‑1                                                                                                                                        CGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGC                <  1:182018/136‑1                                                                                                                                          GGCGGCGCTCTTTCTCCCTGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCC              <  2:1008604/136‑1                                                                                                                                          GGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCC              <  1:679938/136‑1                                                                                                                                          GGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCC              <  1:545875/136‑1                                                                                                                                          GGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCC              <  1:1069718/136‑1                                                                                                                                          GGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCC              <  1:1067659/136‑1                                                                                                                                            gGGCGCTCGATCTCACAGGCGCTGAAACTCTCCGGGCGAACACCTCCCTGGCGCTGAAAATCCCCCGGCGAACACCTCACAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCAT            <  2:1048269/135‑1                                                                                                                                                      TCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATAC  <  2:324026/136‑1                                                                                                                                                                                                                                                                                               GCAGTAGGAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652633‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCATTGCCCTATAC  <  NC_002947/4810126‑4809995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.