New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 652785	29 (1.290)	39 (2.040)	11/224	0.4	76.0%	coding (1961/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4813153	0 (0.000)					intergenic (‑268/‑287)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2

GAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652640‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCAT  <  NC_002947/4813153‑4813032                                                                                                                                                                                                                                                                              cAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGC                                                                                                                                      <  1:227930/135‑1         tctAAAACTGGCGGCGCATGGGGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCGGCTAAGCGCCGCGCGGGCGGCGCTCGATC                                                                                                                              <  1:483918/133‑1         TGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATC                                                                                                                              >  1:455154/1‑136         TGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTAACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATC                                                                                                                              >  1:186310/1‑136                                                                  aatccCGCAGGAATAATTGGCCCTAAACAAACTTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCGGGCGCTGAAAATCCCCCGGC                                                                     <  1:141111/131‑1                                                                            GAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       >  1:233409/1‑76                                                                            GAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       <  2:233409/76‑1                                                                             AATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGC                                                                                                                      >  2:117325/1‑76                                                                             AATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGC                                                                                                                      <  1:117325/76‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACGCCTCCCAGGCGCTGAAAATCCCCCGGC                                                                     <  2:464937/124‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACGCCTCCCAGGCGCTGAAAATCCCCCGGC                                                                     >  1:464937/1‑124                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGC                                                                                                                      <  2:3133/75‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGC                                                                                                                      >  1:3133/1‑75                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       >  2:543312/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       >  2:497504/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       >  2:300955/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       <  1:66910/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       <  1:543312/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       <  1:497504/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       >  2:66910/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGG                                                                                                                       <  1:300955/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAAATCCTCCGGCAAA                                                                                                  <  1:430522/95‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAAATCCTCCGGCAAA                                                                                                  >  2:430522/1‑95                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  2:425626/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  2:303530/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  1:358246/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  1:389371/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  2:358246/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  2:389371/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  1:64522/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  1:425626/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  1:303530/74‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  2:64522/1‑74                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCGCGATCTCCCAGGCGCTGAAACTATCCCGGCGAACACCTACCGGGCGCTGTAAATCCCCCGGCGAACACCTCaaa                                                         >  2:141111/1‑133                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCG                                                                                                                                     <  1:148640/60‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCG                                                                                                                                     <  1:311429/60‑1                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCG                                                                                                                                     >  2:311429/1‑60                                                                              ATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCG                                                                                                                                     >  2:148640/1‑60                                                                               TAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       <  1:395098/73‑1                                                                               TAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGG                                                                                                                       >  2:395098/1‑73                                                                                         GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCTGCGCG                                                                                                                                            >  2:208243/1‑42                                                                                         GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCTGCGCG                                                                                                                                            <  1:208243/42‑1                                                                                         GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGAT                                                                                                                               <  2:447450/55‑1                                                                                         GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGAT                                                                                                                               >  1:447450/1‑55                                                                                          AAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAACTCTCCCGGCGCACACCTCCCAGGCGCTGAAAATCCCCCCGCCAACACCTCCCAGGCGCTGAAAAC                                             >  2:455914/1‑136                                                                                           AACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCACGATCTCCCAGGCGCTGAAACACTCCCGGCGAACACCACCCAGGCGCAGAAAAACCCCCGGCGAAAACCACCCAGGCGCAGAAAACC                                            >  2:541948/1‑136                                                                                                   TAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCA                                    <  2:359445/136‑1                                                                                                             TTTAGCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACC                          <  1:541948/136‑1                                                                                                               TACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTATCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCG                        >  1:51150/1‑136                                                                                                                        AGCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGC               >  2:223032/1‑136                                                                                                                         GCGCCGCGCGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCCGGCGCTGAAAATACCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCc              >  1:446683/1‑135                                                                                                                                 CGGGCGGCGCTCGATCTCCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGC      <  1:78041/136‑1                                                                                                                                     CGGCGCTCGATCTCACAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCAT  <  1:422757/136‑1                                                                                                                                                                                                                                                                              GAACAGCATGAAAAACAGGCGGCGCATGGCGGACTCGCGAGGTGGAACGTGCCCGGCATGATAACGGATGCGCAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/652640‑652785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcgggcggcgctcgatctcCCAGGCGCTGAAACTCTCCCGGCGAACACCTCCCAGGCGCTGAAAATCCCCCGGCGAACACCTCCCAGGCGCTGAAAACCTCCCGCCAAACACCTACCCGCCAAAGCGCGAATTCCGCCCAT  <  NC_002947/4813153‑4813032

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.