New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4982403	54 (0.920)	3 (0.050)	3/250	NT	5.9%	coding (279/702 nt)	flgD	flagellar basal‑body rod modification protein FlgD
	?	NC_002947	= 4982461	45 (0.800)					coding (221/702 nt)	flgD	flagellar basal‑body rod modification protein FlgD

CTTCATGTCCTTGCTGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCCGGCGGCGCCGGTAGAGC  >  NC_002947/4982316‑4982602                                                                                                                                                   |                                                                                                                                              cTTCATGTCCTTGCTGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTcca                                                                                                                                            >  1:157924‑M2/1‑146 (MQ=255) cTTCATGTCCTTGCTGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTcca                                                                                                                                            >  2:172640‑M2/1‑146 (MQ=255)       gTCCTTGCTGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGgctgc                                                                                                                                      >  8:286546/1‑149 (MQ=255)               tGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTccag                                                                                                                                           >  3:70674‑M2/1‑132 (MQ=255)               tGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTccag                                                                                                                                           <  4:70674‑M2/136‑5 (MQ=255)               tGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGCCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTgc                                                                                                                              >  2:67108/1‑149 (MQ=255)                 gTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTgcgc                                                                                                                            <  7:286546/149‑1 (MQ=255)                    tCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCa                                                                                                                          >  7:144706/1‑148 (MQ=255)                        ccACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTgg                                                                                                                     <  2:60206/149‑1 (MQ=255)                         cacaGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTgg                                                                                                                     >  3:236109/1‑148 (MQ=255)                         cacaGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTgg                                                                                                                     <  4:236109/148‑1 (MQ=255)                          acaGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGc                                                                                                                   <  2:27148/149‑1 (MQ=255)                                   tCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGcc                                                                                                                  <  6:361985/141‑1 (MQ=255)                                   tCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGcc                                                                                                                  >  5:361985/1‑141 (MQ=255)                                         tGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGgctg                                                                                                                                       >  3:270533/1‑114 (MQ=255)                                         tGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGgctg                                                                                                                                       <  4:270533/114‑1 (MQ=255)                                              aaTGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGGTACGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTcc                                                                                                >  1:105678/1‑149 (MQ=255)                                              aaTGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGttt                                                                                                   <  5:198931/145‑1 (MQ=255)                                              aaTGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGttt                                                                                                   >  6:198931/1‑145 (MQ=255)                                                 gACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGc                                                                                                                   >  2:175315/1‑126 (MQ=255)                                                 gACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGc                                                                                                                   <  1:175315/126‑1 (MQ=255)                                                     ttGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCAc                                                                                                                <  8:337351/125‑1 (MQ=255)                                                     ttGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCAc                                                                                                                >  7:337351/1‑125 (MQ=255)                                                         gcCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGACCTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCgcgc                                                                                    >  8:240962/1‑149 (MQ=255)                                                         gcCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCTCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGc                                                                                    >  4:176396/1‑149 (MQ=255)                                                         gcCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGc                                                                                    >  1:174013/1‑149 (MQ=255)                                                         gcCCGACCAGCGAGGAGGACTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGATTTCCTGCGGGTCGAGc                                                                                    >  8:158706/1‑149 (MQ=255)                                                           ccGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGCCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCgg                                                                                  <  1:67108/149‑1 (MQ=255)                                                               ccAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGggttc                                                                              >  4:235806/1‑149 (MQ=255)                                                                cAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGGATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGggttct                                                                             >  1:67661/1‑149 (MQ=255)                                                                cAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGCACTCGCCGTTTTCCTGCGGGTCGAGCGggttct                                                                             >  8:77448/1‑149 (MQ=255)                                                                 aGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCACCTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGggttctg                                                                            >  7:164141/1‑149 (MQ=255)                                                                  gCGAGGAGTCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGGGATGTAGGTCACAGCGTCGTTCAGCGTCTGCATGCTTTCCAGGCTGCTGAACTGCGCCATCTGGGCGTCGAACTCGCCGTTTTCCTGCGGGTCGAGCGggttctgg                                                                           <  4:56538/149‑1 (MQ=255)                                                                           ccTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATc                                                                  <  2:105678/149‑1 (MQ=255)                                                                             tGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTccaggccttgcaggactcctcgctggtcgggcgcaatgtcattgtccagaccgacaaggctgtggtcgattccagcaag                                                                <  5:8216‑M2/149‑80 (MQ=255)                                                                              gCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTgg                                                               >  3:2091/1‑149 (MQ=255)                                                                                aaGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGt                                                             <  2:174013/149‑1 (MQ=255)                                                                                aaGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGGCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACTAACTCTCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGt                                                             <  7:158706/149‑1 (MQ=255)                                                                                 aGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTccaggccttgcaggcctcctcgctggtcgggcgcaatgtcattgtccagaccgacaaggctgtggtcgataccagcaaggaca                                                            <  1:228438‑M2/149‑84 (MQ=255)                                                                                     cTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTg                                                            <  4:100037/145‑1 (MQ=255)                                                                                     cTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTg                                                            >  3:100037/1‑145 (MQ=255)                                                                                        ggAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGc                                                      >  4:289580/1‑148 (MQ=255)                                                                                                  aGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTccaggccttgcaggcctcctcgctggtcgggcgcaatgtcattgtccagaccgacaaggctgtggtcgataccagcaaggacatgaagggctcggtcaac                                           >  2:228438‑M2/1‑49 (MQ=255)                                                                                                   gCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCTCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAAc                                          <  7:240962/149‑1 (MQ=255)                                                                                                   gCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAAc                                          >  1:235439/1‑149 (MQ=255)                                                                                                   gCCCGG‑CCGCGATGGAGGGCCCAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAAc                                          <  8:144706/149‑1 (MQ=255)                                                                                                     ccGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAAcgc                                        >  2:357103/1‑149 (MQ=255)                                                                                                              gATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAAc                                                   >  8:7783/1‑130 (MQ=255)                                                                                                              gATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAAc                                                   <  7:7783/130‑1 (MQ=255)                                                                                                                        acaGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTg                                                                                              <  4:55931/77‑1 (MQ=255)                                                                                                                          aGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGc                    <  4:2091/149‑1 (MQ=255)                                                                                                                             gtcgtTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCcgg                 <  2:235439/149‑1 (MQ=255)                                                                                                                                      cGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCCGGCGGCGCCgg        <  1:357103/149‑1 (MQ=255)                                                                                                                                            cATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCCAGCGGCGCCGGTAGAGc  <  3:176396/149‑1 (MQ=255)                                                                                                                                            cATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTCACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCCGGCGGCGCCGGTAGAGc  >  5:273793/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                              CTTCATGTCCTTGCTGGTATCGACCACAGCCTTGTCGGTCTGGACAATGACATTGCGCCCGACCAGCGAGGAGGCCTGCAAGGCCTGGGAAGATTGCAGCCCGG‑CCGCGATGTAGGTCACAGCGTCGTTCAGCGACTGCATGCTTTCCAGGCTGCTGAACTGCGCCAACTGGGCCACGAACTCGCCGTTTTCCTGCGGGTCGAGCGGGTTCTGGTTCTGCATCTGGGTGACCAGCAACTGCAGGAACGCGTCCTTGCCCAGCGCGCTGCCGGCGGCGCCGGTAGAGC  >  NC_002947/4982316‑4982602

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.