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

AAAGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGC  >  NC_002947/4949951‑4950234                                                                                                                                         |                                                                                                                                                     aaaGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGccac                                                                                                                                          >  3:19822/1‑149 (MQ=255) aaaGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTAATCGCCGAACTTCCTGACCTGCACGcccc                                                                                                                                          >  6:245442/1‑147 (MQ=255)   aGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGAc                                                                                                                                                     <  1:167910/136‑1 (MQ=255)   aGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGAc                                                                                                                                                     >  2:167910/1‑136 (MQ=255)     aaaTTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGccacccac                                                                                                                                      >  2:5176/1‑149 (MQ=255)           tCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCa                                                                                                                                 <  5:245442/148‑1 (MQ=255)              accaGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGt                                                                                                                              >  8:235729/1‑148 (MQ=255)                  gCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCagcg                                                                                                                         <  4:19822/149‑1 (MQ=255)                      gAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCagcggag                                                                                                                      <  1:189918/148‑1 (MQ=255)                         cacCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAgcggc                                                                                                                  >  2:47624/1‑149 (MQ=255)                            cAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAgcggcg                                                                                                                 >  1:147235/1‑147 (MQ=255)                                 aagctacgacctgaccagtcaggaccgtatcgtgcggggtcgcatgccgaccctggaaatgatcaacgagcgcttcgcccgctatacccgtatcagcatgttcaACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAgg                                                                                                          >  5:76139‑M1/105‑149 (MQ=255)                                  ggCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAgg                                                                                                          <  8:97809/148‑1 (MQ=255)                                   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                                                                                           >  8:110540/1‑149 (MQ=255)                                                aCAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATa                                                                                           >  5:226795/1‑149 (MQ=255)                                                 cAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATAc                                                                                          <  5:312053/149‑1 (MQ=255)                                                  aGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGAt                                                                                            <  7:30249/146‑1 (MQ=255)                                                  aGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGAt                                                                                            >  8:30249/1‑146 (MQ=255)                                                        gTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGTGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGta                                                                                     >  1:53788/1‑147 (MQ=255)                                                          cgtatcgtgcggggtcgcatgccgaccctggaaatgatcaacgagcgcttcgcccgctatacccgtatcagcatgttcaACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGcagcag                                                                                                           >  3:94901‑M1/80‑123 (MQ=255)                                                          cgtatcgtgcggggtcgcatgccgaccctggaaatgatcaacgagcgcttcgcccgctatacccgtatcagcatgttcaACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGcagcag                                                                                                           <  4:94901‑M1/44‑1 (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                                                             <  5:2291/134‑1 (MQ=255)                                                                                             tggtggGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATc                                                             >  6:2291/1‑134 (MQ=255)                                                                                               gtggGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGc                                              <  4:223654/147‑1 (MQ=255)                                                                                                   gCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGa                                       >  8:158936/1‑149 (MQ=255)                                                                                                   gCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCAACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGa                                       >  4:282670/1‑149 (MQ=255)                                                                                                      cGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGAccc                                    <  2:53788/149‑1 (MQ=255)                                                                                                      cGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGAccc                                    <  5:298734/149‑1 (MQ=255)                                                                                                       gTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGAcccc                                   <  7:158936/149‑1 (MQ=255)                                                                                                       gTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGAcccc                                   >  3:180350/1‑149 (MQ=255)                                                                                                          cAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTC‑GCATGCCGAccctgg                                 <  1:37853/148‑4 (MQ=255)                                                                                                            gCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTC‑GCATGCCGAccctggaaa                              <  6:226795/149‑7 (MQ=255)                                                                                                              gAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCAt                                                           <  2:127412/119‑1 (MQ=255)                                                                                                              gAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCAt                                                           >  1:127412/1‑119 (MQ=255)                                                                                                                    aCGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCAc                               <  6:41903/140‑1 (MQ=255)                                                                                                                    aCGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCAc                               >  5:41903/1‑140 (MQ=255)                                                                                                                         ttCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGAc                 <  3:223867/149‑1 (MQ=255)                                                                                                                                     cATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGACTGGTCAGGTCg      <  7:110540/148‑1 (MQ=255)                                                                                                                                      aTGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTa    <  8:116901/149‑1 (MQ=255)                                                                                                                                         ACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGc  >  7:235729‑M1/1‑148 (MQ=255)                                                                                                                                         |                                                                                                                                                     AAAGAAATTGTCCACCAGCTTGAACACCAGCTTGGCGTCGAGGATGAACAGCGAAGTGCCGCGCAGCGGCTTGATCTTGACCAGGTTGAGGCTGGTGGGCACGTACAGCGAGTGCACGTATTCGCCGAACTTCATGACCTGCACGCCACCCACGGCCACGTCAGCGGAGCGGCGCAGCAGGTTGAACATGCTGATACGGGTATAGCGGGCGAAGCGCTCGTTGATCATTTCCAGGGTCGGCATG‑CGACCCCGCACGATACGGTCCTGACTGGTCAGGTCGTAGC  >  NC_002947/4949951‑4950234

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ 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.