New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4979899	33 (0.600)	4 (0.080)	4/246	NT	10.3%	coding (311/741 nt)	flgF	flagellar basal‑body rod protein FlgF
	?	NC_002947	= 4979934	38 (0.710)					coding (276/741 nt)	flgF	flagellar basal‑body rod protein FlgF

CCACTTCCACTTTCTGCTCCGGCGGGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATC  >  NC_002947/4979795‑4980081                                                                                                                                            |                                                                                                                                                    ccacttccacttTCTGCTCCGGCGGGATGGCGCTCGGGCCACCGTTGCGGATCACCGGCATGCCATTGCCGGCACGCAGCACCCCGAGGGCCTCGATGTTCAGGCTACCGGTACGCACTTAGGCTTCGCTGCCGTCCGGCGCCTGCACg                                                                                                                                            >  4:197891/1‑149 (MQ=255)       ccacttTCTGCTCCGGCGGGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGa                                                                                                                                        <  7:323762/147‑1 (MQ=255)       ccacttTCTGCTCCGGCGGGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGAt                                                                                                                                       >  6:5853/1‑148 (MQ=255)        cacttTCTGCTCCGGCGGGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATaa                                                                                                                                     <  1:329788/149‑1 (MQ=255)                     ggcggGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGt                                                                                                                        >  8:216874/1‑149 (MQ=255)                                      gCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCAcc                                                                                                                    >  8:77096/1‑136 (MQ=255)                                      gCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCAcc                                                                                                                    <  7:77096/136‑1 (MQ=255)                                      gCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGt                                                                                                       >  3:348415/1‑149 (MQ=255)                                          ccGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTcgcg                                                                                                   <  4:348415/149‑1 (MQ=255)                                            gTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGc                                                                                                 <  7:216874/149‑1 (MQ=255)                                                      aCCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCa                                                                                               <  3:221842/141‑1 (MQ=255)                                                      aCCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCa                                                                                               >  4:221842/1‑141 (MQ=255)                                                      aCCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGa                                                                                        <  2:53184/148‑1 (MQ=255)                                                          gCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAAc                                                                                   >  7:179827/1‑149 (MQ=255)                                                            aTGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACgg                                                                                 <  8:179827/149‑1 (MQ=255)                                                                 aTTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCtt                                                                            <  5:5853/149‑1 (MQ=255)                                                                  ttGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGcc                                                                                                                           >  1:307727/1‑101 (MQ=255)                                                                  ttGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGcc                                                                                                                           <  2:307727/101‑1 (MQ=255)                                                                                   acCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCg                                                          >  5:265526/1‑149 (MQ=255)                                                                                     cGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCggg                                                        >  5:337956/1‑149 (MQ=255)                                                                                         ggCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTcgc                                                                                                    >  7:290931/1‑101 (MQ=255)                                                                                         ggCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTcgc                                                                                                    <  8:290931/101‑1 (MQ=255)                                                                                            aTCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCgg                                                 >  7:22615/1‑149 (MQ=255)                                                                                             tCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCgcctgaacatcgatgccctcggtgtgctgcgtgccggcaatggcatgccggtgatcggcaacggtggcccgatcgccatcccgccg                                                               >  2:85281‑M2/1‑48 (MQ=255)                                                                                             tCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCgactgaacatcgatgccctcggtgtgctgcgtgccggcaatggcatgccggtgatcggcaacggtggcccgatcgccatcccgccg                                                               <  1:85281‑M2/134‑87 (MQ=255)                                                                                              ccaTGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCAATTGCCGGTCACCGCCAGGTCAAGGTCGCGGCCAGTTTCGAGCAACGGGCCTTCACTGAAGTCGGTGGACGGGAGATCGGt                                                >  4:81755/3‑148 (MQ=255)                                                                                               gATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCgcctgaacatcgatgccctcggtgtgctgcgtgccggcaatggcatgccggtgatcggcaacggtggcccgatcgccatcccgccggagcagaaagt                                                    >  4:335400‑M2/1‑46 (MQ=255)                                                                                               gATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCgcctgaacatcgatgccctcggtgtgctgcgtgccggcaatggcatgccggtgatcggcaacggtggcccgatcgccatcccgccggagcagaaagt                                                    <  3:335400‑M2/143‑98 (MQ=255)                                                                                                aTGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCAt                                             >  5:35191/1‑149 (MQ=255)                                                                                                aTGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCAt                                             >  8:245549/1‑149 (MQ=255)                                                                                                                  cGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCg                            <  7:303851/148‑1 (MQ=255)                                                                                                                    cacaTAGGCTTCGCTGCCGGCCGGCGCCTGCCCGGCGATAAAGCCTTTGCCGGTCACCGCCACGGCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGaa                         <  3:261406/149‑1 (MQ=255)                                                                                                                     acaTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGCCCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCTGa                          >  8:331475/1‑147 (MQ=255)                                                                                                                     acaTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCtt                                                                            <  4:87330/97‑1 (MQ=255)                                                                                                                     acaTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCtt                                                                            >  3:87330/1‑97 (MQ=255)                                                                                                                     acaTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGa                          >  5:306240/1‑147 (MQ=255)                                                                                                                     acaTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGGTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGaaa                        <  3:197891/149‑1 (MQ=255)                                                                                                                      caTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAg                       <  6:306240/149‑1 (MQ=255)                                                                                                                       aTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACgcgc                              <  4:326567/141‑1 (MQ=255)                                                                                                                       aTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACgcgc                              >  3:326567/1‑141 (MQ=255)                                                                                                                       aTAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGc                      >  2:214973/1‑149 (MQ=255)                                                                                                                           gCTTCGCTGCCGTCCGGCGCCTGCACGGGGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGt                   >  1:199147/1‑148 (MQ=255)                                                                                                                             ttCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCAc                >  7:185705/1‑149 (MQ=255)                                                                                                                                           gcgcCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATc  >  4:197098/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                    CCACTTCCACTTTCTGCTCCGGCGGGATGGCGATCGGGCCACCGTTGCCGATCACCGGCATGCCATTGCCGGCACGCAGCACACCGAGGGCATCGATGTTCAGGCTACCGGTACGCACATAGGCTTCGCTGCCGTCCGGCGCCTGCACGGCGATAAAGCCTTTGCCGGTCACCGCCACGTCAAGGTCGCGGCCAGTTTCGACCAACGGGCCTTCACTGAAGTCGGTGGCCGGGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATC  >  NC_002947/4979795‑4980081

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.