New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4978911 =	42 (0.700)	5 (0.090)	5/250	NT	12.4%	coding (511/786 nt)	flgG	flagellar basal‑body rod protein FlgG
	?	NC_002947	4978950 =	31 (0.550)					coding (472/786 nt)	flgG	flagellar basal‑body rod protein FlgG

CAGCGTCTGCTGCAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAG  >  NC_002947/4978765‑4979053                                                                                                                                                    |                                                                                                                                                cAGCGTCTGCTGCAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑g                                                                                                                                               >  2:276290/1‑148 (MQ=255) cAGCGTCTGCTGCAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑Ga                                                                                                                                              >  8:122311/1‑149 (MQ=255)      accgtgtcgtatacccgtgacggtaccttccacctgaactccgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCAc                                                                                                                                          <  6:167380‑M1/7‑1 (MQ=255)            gcAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCtgtg                                                                                                                                     >  3:276977/1‑147 (MQ=255)             cAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCAccaccgccg                                                                                                                                  >  6:152773/1‑142 (MQ=255)                ggtggtGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCg                                                                                                                               >  5:98724/1‑149 (MQ=255)                  tggtgCCTAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCggg                                                                                                                             <  7:77305/149‑1 (MQ=255)                  tggtgCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCggg                                                                                                                             <  7:122311/149‑1 (MQ=255)                    gtgCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGtt                                                                                                                           <  5:45727/149‑1 (MQ=255)                     tgCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTg                                                                                                                          >  1:366531/1‑149 (MQ=255)                         aaaaCCGTTCAGGCCTGGGGTGCCGACCTGAGGTGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCcgg                                                                                                                      >  1:49358/1‑149 (MQ=255)                         aaaaCCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCcgg                                                                                                                      >  1:310417/1‑149 (MQ=255)                         aaaaCCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCcgg                                                                                                                      >  6:116571/1‑149 (MQ=255)                             ccGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCggt                                                                                                                  <  2:310417/149‑1 (MQ=255)                              cGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCggtg                                                                                                                 <  2:366531/149‑1 (MQ=255)                                cttccacctcaactccgacggccagatcgtcactgacaacggctacgccctggaccctgccattgccgtgcctaacgacgcgccgaccttcaccgttgggcaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCggtgg                                                                                                                >  2:99611‑M1/117‑149 (MQ=255)                                    ctcctgttctgcgacggcatgatcgtcactgataacggcttcgccctggagcctgccattgtcgtgcctcacgacgcgcagagcttgaccgttgtgcaggacggcagcgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGAt                                                                                                            >  4:56803‑M1/113‑149 (MQ=255)                                     gCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATc                                                                                                           >  7:5596/1‑148 (MQ=255)                                     gCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATc                                                                                                           >  5:352616/1‑148 (MQ=255)                                     acctgatctccgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATc                                                                                                           >  8:16074‑M1/112‑149 (MQ=255)                                       cTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGTCAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGa                                                                                                         <  1:107006/149‑1 (MQ=255)                                               cgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGaca                                                                                                       <  7:275368‑M1/42‑1 (MQ=255)                                               cgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGaca                                                                                                       >  8:275368‑M1/102‑143 (MQ=255)                                                               cACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGt                                                                                 >  5:342439/1‑148 (MQ=255)                                                                    gcggcgGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAg                                                                             <  8:5596/147‑1 (MQ=255)                                                                    gcggcgGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAg                                                                             <  1:139133/147‑1 (MQ=255)                                                                     cggcggTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTc                                                                          <  2:49358/149‑1 (MQ=255)                                                                               gAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTTCGcgtcgt                                                                >  5:167380/1‑149 (MQ=255)                                                                               gAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGcgtcgt                                                                >  4:8214/1‑149 (MQ=255)                                                                                 ggAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTa                                                              <  2:7707/149‑1 (MQ=255)                                                                                   aaCAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAgg                                                            >  6:24457/1‑149 (MQ=255)                                                                                    aCAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAgg                                                            >  2:65159/1‑148 (MQ=255)                                                                                        gTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGa                                                       >  2:200410/1‑149 (MQ=255)                                                                                              gCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATgg                                                 <  1:276290/149‑1 (MQ=255)                                                                                              gCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATgg                                                 >  2:297141/1‑149 (MQ=255)                                                                                                   tCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGc                                            >  6:91561/1‑149 (MQ=255)                                                                                                      ccTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGATCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTc                                          >  1:38879/1‑148 (MQ=255)                                                                                                       cTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCa                                        <  3:8214/149‑1 (MQ=255)                                                                                                        tGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAg                                       >  5:125463/1‑149 (MQ=255)                                                                                                         gCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCCGGTTCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAg                                       >  1:265040/1‑149 (MQ=255)                                                                                                         gCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAgg                                      <  5:116571/149‑1 (MQ=255)                                                                                                          cAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAg                                       <  6:342439/147‑1 (MQ=255)                                                                                                           aGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGc                                    <  8:333000/149‑1 (MQ=255)                                                                                                              ccggccggGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTa                                 <  5:24457/149‑1 (MQ=255)                                                                                                                ggccggGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGc                               >  1:35928/1‑149 (MQ=255)                                                                                                                    gggTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGtt                           <  1:65159/149‑1 (MQ=255)                                                                                                                              aaGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGa                   <  4:276977/148‑1 (MQ=255)                                                                                                                                              tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAg  <  6:352616/149‑1 (MQ=255)                                                                                                                                              tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAg  <  6:98724/149‑1 (MQ=255)                                                                                                                                              tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGACAACGGTGAAGGTCTGCGCGTCGTTAGGAACGACAAGGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAg  >  2:117217/1‑149 (MQ=255)                                                                                                                                               gTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                       <  3:6191/127‑1 (MQ=255)                                                                                                                                               gTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                       >  4:6191/1‑127 (MQ=255)                                                                                                                                                    |                                                                                                                                                CAGCGTCTGCTGCAAGGTGGTGCCAAAACCGTTCAGGCCTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAG  >  NC_002947/4978765‑4979053

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.