New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4959601	37 (0.820)	4 (0.090)	4/240	NT	10.4%	coding (915/1779 nt)	fliF	flagellar M‑ring protein
	?	NC_002947	= 4959615	33 (0.760)					coding (901/1779 nt)	fliF	flagellar M‑ring protein

GAATGGCAGCAGCCGGGGTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAATGTTGTGCACACGCTGGGTGAGCATGCTTTC  >  NC_002947/4959456‑4959741                                                                                                                                                  |                                                                                                                                              gAATGGCAGCAGCCGGGGGAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCg                                                                                                                                           >  1:347017/1‑150 (MQ=255)   aTGGCAGCAGCCGGGGTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGc                                                                                                                                         <  2:427064/150‑1 (MQ=255)           agcCGGGGTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCggg                                                                                                                                 <  1:53134/150‑1 (MQ=255)                  gTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCg                                                                                                                                   <  2:425317/141‑1 (MQ=255)                  gTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCg                                                                                                                                   >  1:425317/1‑141 (MQ=255)                  gTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAAc                                                                                                                          >  1:608869/1‑150 (MQ=255)                        gcgcCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCg                                                                                                                    >  1:1098408/1‑150 (MQ=255)                        gcgcCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCg                                                                                                                    <  1:926717/150‑1 (MQ=255)                             accaGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGGCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGt                                                                                                               <  2:487219/150‑1 (MQ=255)                                                    cggcgCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGa                                                                                       >  1:648719/1‑150 (MQ=255)                                                    cggcgCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGa                                                                                       <  1:531797/150‑1 (MQ=255)                                                      gcgcCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAgg                                                                                     <  2:403802/150‑1 (MQ=255)                                                        gcCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTc                                                                                   >  2:632900/1‑150 (MQ=255)                                                            ggcggcTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGaa                                                                                                                           <  1:1144551/107‑1 (MQ=255)                                                            ggcggcTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGaa                                                                                                                           >  2:1144551/1‑107 (MQ=255)                                                                  tGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGGTCCCAGCGCTGCTCCGGCTGGTAGGGGTTGTAGT‑CTCGGAAGTGGGATTCGACCTCGCTAAAGTCGAGGTCGGCAGACACt                                                                         >  1:570023/1‑150 (MQ=255)                                                                     ttGCTGAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCg                                                                      <  1:495688/150‑1 (MQ=255)                                                                         ttaGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCt                                                                  >  2:600845/3‑150 (MQ=255)                                                                                 ccAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCgg                                                          >  1:1075521/1‑150 (MQ=255)                                                                                      cgcacCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGtt                                                     <  2:658529/148‑1 (MQ=255)                                                                                       acacCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACcccgaccagccggcgttgcgc                                                                                                                          >  1:49146‑M1/1‑60 (MQ=255)                                                                                       acacCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACcccgaccagccggcgttgcgc                                                                                                                          <  2:49146‑M1/81‑22 (MQ=255)                                                                                       acacCTTGCGGGCCTTGGCTGATGGCATGCTGGTCATCTACCGACTGGTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGACCTTGTAGCGGTCGTTg                                                    <  2:615300/150‑1 (MQ=255)                                                                                         acCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCg                                                                      <  1:360218/130‑1 (MQ=255)                                                                                         acCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCg                                                                      >  2:360218/1‑130 (MQ=255)                                                                                          ccTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGccc                                                 <  2:648719/150‑1 (MQ=255)                                                                                           cTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCa                                                >  2:673410/1‑150 (MQ=255)                                                                                                gggCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACcccgaccagccggcgttgcgca                                                                                                                         >  2:1010406‑M1/1‑51 (MQ=255)                                                                                                gggCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACcccgaccagccggcgttgcgca                                                                                                                         <  1:1010406‑M1/73‑23 (MQ=255)                                                                                                   ccTTGGCTGCTGGTTCGTTGTAAGTCGACGGACTGCTCGCTGCGCTACGCCGGCTGGTCGGGGTTGACCCGTTCCGAGGT‑GCACTCGACCGCGCTTACGTCGCGCTCCGCGGACACTTCTGCATTGTAGCAGTCGTTGTACCCCACCGGc                                        <  2:570023/150‑1 (MQ=255)                                                                                                     ttGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTg                                      >  1:461211/1‑150 (MQ=255)                                                                                                         ctgctgGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGa                                  >  2:263091/1‑150 (MQ=255)                                                                                                            ctgGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTTTAGCGGTCGTTGCCCAACACCGGCTGCAGAAtg                               >  2:180135/1‑150 (MQ=255)                                                                                                                cACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAAtgttgt                           >  1:576797/1‑150 (MQ=255)                                                                                                                 aCGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCCAACGCTTTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAATGTtgtg                          <  2:347017/150‑1 (MQ=255)                                                                                                                             gaccgacTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCgg                                                          <  2:413095/106‑1 (MQ=255)                                                                                                                             gaccgacTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCgg                                                          >  1:413095/1‑106 (MQ=255)                                                                                                                               ccgacTGCTCGCTGCTCTTTGCCGGTTGGTCGGGGTTGTACTGTTCGGAGGT‑GGTCGCGACCGCGCTGAAGTCGAGGTCGGCGGACATTTCGGGCTTGTAGCTGTCGTTGACGAACACCGGCTGCAGAATGTTGTGCACACGCTGGGTGa            <  2:579569/150‑1 (MQ=255)                                                                                                                                    tGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAATGTTGTGCACACGCTGGGTGAGCATg       >  2:359380/1‑150 (MQ=255)                                                                                                                                       tCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCtt                                                                 <  1:527483/89‑1 (MQ=255)                                                                                                                                       tCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCtt                                                                 >  2:527483/1‑89 (MQ=255)                                                                                                                                         gCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAATGTTGTGCACACGCTGGGTGAGCATGCTTTc  <  1:359380/150‑1 (MQ=255)                                                                                                                                           tGCGCAACGCCGGCTGGTCGGGgttgcgcagcgagcagtcggtcgacgaacaacgtgccagcagccaaggccc                                                                              >  2:1010406‑M2/1‑22 (MQ=255)                                                                                                                                           tGCGCAACGCCGGCTGGTCGGGgttgcgcagcgagcagtcggtcgacgaacaacgtgccagcagccaaggccc                                                                              <  1:1010406‑M2/73‑52 (MQ=255)                                                                                                                                            gcgcAACGCCGGCTGGTCGGGgttgcgcagcgagcagtcggtcgacgaacaacgtgccagcagccaaggcccgcaaggtgt                                                                     <  2:49146‑M2/81‑61 (MQ=255)                                                                                                                                            gcgcAACGCCGGCTGGTCGGGgttgcgcagcgagcagtcggtcgacgaacaacgtgccagcagccaaggcccgcaaggtgt                                                                     >  1:49146‑M2/1‑21 (MQ=255)                                                                                                                                                  |                                                                                                                                              GAATGGCAGCAGCCGGGGTAGCCGCGCCACCAGTGGTCTGCGGTGCCGAAGCGGCGCCTGGCGGCTGGTTGCTCAGCGCGCCAGGCACACCTTGCGGGCCTTGGCTGCTGGCACGTTGTTCGTCGACCGACTGCTCGCTGCGCAACGCCGGCTGGTCGGGGTTGAACTGTTCGGAGGT‑GGACTCGACCGCGCTGAAGTCGAGGTCGGCGGACACTTCGGCCTTGTAGCGGTCGTTGCCCAACACCGGCTGCAGAATGTTGTGCACACGCTGGGTGAGCATGCTTTC  >  NC_002947/4959456‑4959741

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