New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4956132	56 (1.010)	3 (0.060)	3/242	NT	5.6%	coding (623/1374 nt)	fliI	flagellum‑specific ATP synthase
	?	NC_002947	= 4956158	49 (0.940)					coding (597/1374 nt)	fliI	flagellum‑specific ATP synthase

GCAGGCGCATCAGCGGCGCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAACGGCTTGCTGATAGG  >  NC_002947/4956016‑4956298                                                                                                                                               |                                                                                                                                             gcAGGCGCATCAGCGGCGCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTtcggtg                                                                                                                                        >  7:275652‑M2/1‑143 (MQ=255)    ggCGCATCAGCGGCGCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGaaa                                                                                                                                     <  8:202048/149‑1 (MQ=255)        cATCAGCGGCGCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACggg                                                                                                                                 >  6:13197/1‑149 (MQ=255)             gcggcgCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGtcatc                                                                                                                            <  4:334309/149‑1 (MQ=255)                    aTCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCa                                                                                                                     <  8:253595/149‑1 (MQ=255)                    aTCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCa                                                                                                                     <  8:202864/149‑1 (MQ=255)                          ggccggcGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATa                                                                                                               >  7:283401/1‑149 (MQ=255)                           gccggcGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATAc                                                                                                              <  8:328938/149‑1 (MQ=255)                              ggcGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGa                                                                                                           >  5:321057/1‑149 (MQ=255)                                      caccaccacCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCca                                                                                                   >  7:123132/1‑149 (MQ=255)                                       accaccaccGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGaaa                                                                                                                                     <  7:313580/114‑1 (MQ=255)                                       accaccaccGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGaaa                                                                                                                                     >  8:313580/1‑114 (MQ=255)                                         caccaccGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCacac                                                                                                <  8:123132/149‑1 (MQ=255)                                         caccaccGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCacac                                                                                                <  2:325346/149‑1 (MQ=255)                                               cGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTAc                                                                                          <  8:283401/149‑1 (MQ=255)                                               cGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTAc                                                                                          <  5:13197/149‑1 (MQ=255)                                               cGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTAACCCACACCGGTAc                                                                                          >  4:55494/1‑149 (MQ=255)                                                 aGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCg                                                                                        >  8:46700/1‑149 (MQ=255)                                                   cgcTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGc                                                                                      >  6:269305/1‑149 (MQ=255)                                                   cgcTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGc                                                                                      <  5:269305/149‑1 (MQ=255)                                                      ttGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGaa                                                                                   >  5:280428/1‑149 (MQ=255)                                                          ggCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTCCCGGCGAACAgg                                                                               >  8:332756/1‑149 (MQ=255)                                                            gccgtcccACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGcc                                                                             <  4:338487/142‑1 (MQ=255)                                                             ccTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGcc                                                                             >  7:259986/1‑148 (MQ=255)                                                              ctctTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCt                                                                            >  3:96102/1‑148 (MQ=255)                                                                    aCCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCt                                                                     <  6:131688/149‑1 (MQ=255)                                                                     ccAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTg                                                                    <  7:45720/149‑1 (MQ=255)                                                                     ccAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTg                                                                    >  1:276387/1‑149 (MQ=255)                                                                      cAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTgg                                                                   >  5:107413/1‑149 (MQ=255)                                                                      cAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTgg                                                                   >  4:110599/1‑149 (MQ=255)                                                                       aaGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTAcc                                                                                         >  8:6502/1‑126 (MQ=255)                                                                       aaGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTAcc                                                                                         <  7:6502/126‑1 (MQ=255)                                                                         ggATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCa                                                                >  6:225265/1‑149 (MQ=255)                                                                         ggATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCa                                                                <  6:321057/149‑1 (MQ=255)                                                                                   gATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTGGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACgg                                                      <  2:161909/149‑1 (MQ=255)                                                                                   gATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACgg                                                      >  1:143531/1‑149 (MQ=255)                                                                                           ccTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAg                                               <  5:225265/148‑1 (MQ=255)                                                                                            cTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTgg                                                                   >  1:345442/1‑127 (MQ=255)                                                                                            cTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTgg                                                                   <  2:345442/127‑1 (MQ=255)                                                                                             ttCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGcc                                            >  4:319465/1‑149 (MQ=255)                                                                                                aCCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGt                                          <  4:157260/148‑1 (MQ=255)                                                                                                         ccccGCTCACCGATCAGGCCGACCCCGATGATTTCGGCTtcggtgagcgggggcgcgaggtgaaggaagtcatcgagcacatccttggtgaagagggcctcaagcgctcggtggtggtggctgcgccggccgacgatgcgccgctgatg                                <  6:201754‑M2/149‑111 (MQ=255)                                                                                                         ccccGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGc                                 >  3:287500/1‑148 (MQ=255)                                                                                                               tCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGcc                          >  6:307445/1‑149 (MQ=255)                                                                                                                cACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGccc                         <  7:192005/149‑1 (MQ=255)                                                                                                                 aCCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCGGTTGATACTGCGAATGCCca                        <  6:280428/149‑1 (MQ=255)                                                                                                                 aCCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGcc                          <  3:319465/147‑1 (MQ=255)                                                                                                                     aTCAGGCCGACCACGATGATTTCGGCTtcggtgagcgggggcgcgaggtgaaggaattcatcgagcacatccttggtgaaga                                                                                       >  7:235049‑M2/1‑27 (MQ=255)                                                                                                                     aTCAGGCCGACCACGATGATTTCGGCTtcggtgagcgggggcgcgaggtgaaggaattcatcgagcacatccttggtgaaga                                                                                       <  8:235049‑M2/82‑56 (MQ=255)                                                                                                                     aTCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGTCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATc                    >  6:106605/1‑149 (MQ=255)                                                                                                                         ggCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCTAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAAc                <  4:96102/149‑1 (MQ=255)                                                                                                                         ggCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAAc                >  3:212891/1‑149 (MQ=255)                                                                                                                         ggCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAAc                <  4:212891/149‑1 (MQ=255)                                                                                                                             gACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAACGGCt            <  4:287500/149‑1 (MQ=255)                                                                                                                                cACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAACGGCTTGc         <  3:55494/149‑1 (MQ=255)                                                                                                                                        tttCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAACGGCTTGCTGATAgg  <  5:106605/148‑1 (MQ=255)                                                                                                                                               |                                                                                                                                             GCAGGCGCATCAGCGGCGCATCGTCGGCCGGCGAAGCCACCACCACCGAGCGCTTGAGGCCCTCTTCACCAAGGATGTGCTCGATGAATTCCTTCACCTCGCGCCCCCGCTCACCGATCAGGCCGACCACGATGATTTCGGCTTCGGTGAAACGGGTCATCATGCCCAGCAATACCGATTTACCCACACCGGTACCGGCGAACAGGCCTAACCGCTGGCCACGGCCGACGGTAAGCAGGCCGTTGATACTGCGAATGCCCACATCCAACGGCTTGCTGATAGG  >  NC_002947/4956016‑4956298

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.