New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4950087 =	43 (0.870)	3 (0.060)	3/244	NT	7.2%	coding (257/969 nt)	fliM	flagellar biosynthesis switching/energizing protein
	?	NC_002947	4950133 =	36 (0.770)					coding (211/969 nt)	fliM	flagellar biosynthesis switching/energizing protein

GCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGATACTGCCAGGCTCGGATGCACTCTCGGT  >  NC_002947/4949985‑4950268                                                                                                                                                     |                                                                                                                                          gCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGtt                                                                                                                                           <  2:104337/149‑1 (MQ=255)      gAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAAc                                                                                                                                       <  1:5176/148‑1 (MQ=255)      gAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAAc                                                                                                                                       <  8:151338/148‑1 (MQ=255)        ggATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATg                                                                                                                                    <  1:47624/149‑1 (MQ=255)              aCAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATa                                                                                                                              >  5:226795/1‑149 (MQ=255)              aCAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATa                                                                                                                              >  8:110540/1‑149 (MQ=255)               cAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATAc                                                                                                                             <  5:312053/149‑1 (MQ=255)                aGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGAt                                                                                                                               >  8:30249/1‑146 (MQ=255)                aGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGAt                                                                                                                               <  7:30249/146‑1 (MQ=255)                      gTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGTGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGta                                                                                                                        >  1:53788/1‑147 (MQ=255)                                     ttGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCATGTTCAACctgctg                                                                                                                                 >  6:169697/1‑123 (MQ=255)                                     ttGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCATGTTCAACctgctg                                                                                                                                 <  5:169697/123‑1 (MQ=255)                                     ttGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTc                                                                                                       >  3:223654/1‑149 (MQ=255)                                                   gTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTc                                                                                           >  6:298734/1‑147 (MQ=255)                                                     tGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAgg                                                                                       >  3:153244/1‑149 (MQ=255)                                                      gAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAgg                                                                                       <  8:36922/148‑1 (MQ=255)                                                         gCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCg                                                                                   <  2:147235/149‑1 (MQ=255)                                                           tggtggGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATc                                                                                                >  6:2291/1‑134 (MQ=255)                                                           tggtggGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATc                                                                                                <  5:2291/134‑1 (MQ=255)                                                             gtggGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGc                                                                                 <  4:223654/147‑1 (MQ=255)                                                                 gCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑Ga                                                                         >  8:158936/1‑149 (MQ=255)                                                                 gCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCAACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑Ga                                                                         >  4:282670/1‑149 (MQ=255)                                                                    cGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GAccc                                                                      <  2:53788/149‑1 (MQ=255)                                                                    cGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GAccc                                                                      <  5:298734/149‑1 (MQ=255)                                                                     gTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GAcccc                                                                     >  3:180350/1‑149 (MQ=255)                                                                     gTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GAcccc                                                                     <  7:158936/149‑1 (MQ=255)                                                                        cAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTC‑GCATGCC‑GAccctgg                                                                   <  1:37853/148‑4 (MQ=255)                                                                          gCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTC‑GCATGCC‑GAccctggaaa                                                                <  6:226795/149‑7 (MQ=255)                                                                            gAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCAt                                                                                              >  1:127412/1‑119 (MQ=255)                                                                            gAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCAt                                                                                              <  2:127412/119‑1 (MQ=255)                                                                                  aCGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCAc                                                                 <  6:41903/140‑1 (MQ=255)                                                                                  aCGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCAc                                                                 >  5:41903/1‑140 (MQ=255)                                                                                       ttCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGAc                                                   <  3:223867/149‑1 (MQ=255)                                                                                                   cATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCg                                        <  7:110540/148‑1 (MQ=255)                                                                                                    aTGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTa                                      <  8:116901/149‑1 (MQ=255)                                                                                                       ACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGc                                    >  7:235729‑M1/1‑148 (MQ=255)                                                                                                        cctgctgcgccgctccgctgacgtggccgtgggtggcgtgcaggtTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCtt                                  >  5:76139‑M2/46‑149 (MQ=255)                                                                                                         ctgctgcgccgctccgctgacgtggccgtgggtggcgtgcaggtTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACg                                                           <  4:94901‑M2/79‑1 (MQ=255)                                                                                                         ctgctgcgccgctccgctgacgtggccgtgggtggcgtgcaggtTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACg                                                           >  3:94901‑M2/45‑123 (MQ=255)                                                                                                           GCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCAc                                                                 >  5:234324‑M1/1‑115 (MQ=255)                                                                                                           GCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCAc                                                                 <  6:234324‑M1/115‑1 (MQ=255)                                                                                                            CACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGa                              >  4:153244‑M1/1‑149 (MQ=255)                                                                                                            CACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCG‑CATG‑CCGaccct                                                                     <  2:10985‑M1/110‑2 (MQ=255)                                                                                                            CACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCG‑CATG‑CCGaccct                                                                     >  1:10985‑M1/1‑109 (MQ=255)                                                                                                                 cacccacGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTAACGTCGTAGCTTTTGATACTg                         >  8:112661/1‑149 (MQ=255)                                                                                                                     cacGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGATACTGCCAg                     <  4:180350/149‑1 (MQ=255)                                                                                                                          ccACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑Ga                                                                         <  4:192900/92‑1 (MQ=255)                                                                                                                          ccACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑Ga                                                                         >  3:192900/1‑92 (MQ=255)                                                                                                                                          gcgcAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCtt                                  >  7:20233/1‑115 (MQ=255)                                                                                                                                          gcgcAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCtt                                  <  8:20233/115‑1 (MQ=255)                                                                                                                                            gcagcaGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGATACTGCCAGGCTCGGATGCACTCTCGGt  <  6:87782/145‑1 (MQ=255)                                                                                                                                            gcagcaGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGATACTGCCAGGCTCGGATGCACTCTCGGt  >  5:87782/1‑145 (MQ=255)                                                                                                                                                     |                                                                                                                                          GCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑C‑GACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGCTTTTGATACTGCCAGGCTCGGATGCACTCTCGGT  >  NC_002947/4949985‑4950268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ 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.