New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4978953 =	38 (1.640)	3 (0.130)	3/246	NT	8.6%	coding (514/786 nt)	flgG	flagellar basal‑body rod protein FlgG
	?	NC_002947	4978998 =	26 (1.140)					coding (469/786 nt)	flgG	flagellar basal‑body rod protein FlgG

GTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGT  >  NC_002947/4978853‑4979141                                                                                                                                                  |                                                                                                                                                tccgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTg                                                                                                                                             <  1:306465‑M1/50‑1 (MQ=255) gTGCCGACCTGAGTCGCGCCACTGGCGGCTGTCTAGAGGAACAGGTTGTCGCCTATCGCCTGCAGGCCGGCCGGGTTGATGAGGTCGGCAGTCTTGATGTGGCCGATCTCCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTg                                                                                                                                             <  1:77659/150‑1 (MQ=255)          cagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTgg                                                                                                                                    >  2:306465‑M1/92‑150 (MQ=255)                gcgcCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACg                                                                                                                              <  1:380545/150‑1 (MQ=255)                   ccACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTg                                                                                                                           <  2:301394/150‑1 (MQ=255)                    cACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGa                                                                                                                          >  2:564459/1‑150 (MQ=255)                     aCTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGaa                                                                                                                         <  1:4906/150‑1 (MQ=255)                      cTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAg                                                                                                                        <  1:329189/150‑1 (MQ=255)                                                   gCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTg                                                                                                                                             >  2:191309/1‑100 (MQ=255)                                                   gCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTg                                                                                                                                             <  1:191309/100‑1 (MQ=255)                                                            cTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAg                                                                                  <  1:280079/150‑1 (MQ=255)                                                                       ccggGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGt                                                                       >  2:295035/1‑150 (MQ=255)                                                                            ttGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGTCGTCCTTGCCAACAGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                                                                  <  2:121012/150‑1 (MQ=255)                                                                            ttGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTgg                                                                                                                                    >  2:13038/1‑84 (MQ=255)                                                                            ttGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTgg                                                                                                                                    <  1:13038/84‑1 (MQ=255)                                                                            ttGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                                                                  <  1:564459/150‑1 (MQ=255)                                                                                tgaAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATgg                                                                                            >  2:111989/1‑120 (MQ=255)                                                                                tgaAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATgg                                                                                            <  1:111989/120‑1 (MQ=255)                                                                                    gTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAg                                                                           <  1:407563/133‑1 (MQ=255)                                                                                    gTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAg                                                                           >  2:407563/1‑133 (MQ=255)                                                                                       ggcggTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAAGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTg                                                       <  1:100786/150‑1 (MQ=255)                                                                                       ccaggacggcaccgtgtcgatcaccaccgccggcaacccggctgcacaggtgatcggcaCGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTg                                                       >  2:306465‑M2/60‑150 (MQ=255)                                                                                           gTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCg                                                   >  2:487207/1‑150 (MQ=255)                                                                                              tGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTc                                                                                                                                        >  1:360886/1‑62 (MQ=255)                                                                                              tGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTc                                                                                                                                        <  2:360886/62‑1 (MQ=255)                                                                                                caccgtgtcgatcaccaccgccggcaacccggctgcacaggtgatcggcaCGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGa                                              <  1:306465‑M2/100‑1 (MQ=255)                                                                                                    ttGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTc                                          <  2:524592/150‑1 (MQ=255)                                                                                                     tgtcgatcaccaccgccggcaacccggctgcacaggtgatcggcaCGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCa                                         >  1:187135‑M2/46‑150 (MQ=255)                                                                                                     TGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCa                                         >  1:487207‑M1/1‑150 (MQ=255)                                                                                                       cccaTCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAgg                                       <  1:522500/147‑1 (MQ=255)                                                                                                                        cGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTgg                                                      >  1:149919/1‑118 (MQ=255)                                                                                                                        cGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTgg                                                      <  2:149919/118‑1 (MQ=255)                                                                                                                         gggTTGCCGGCGGTGGTGATCTACACGGGGGCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGTGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTCGAAGATACCGTCActc                     <  2:434567/150‑3 (MQ=255)                                                                                                                               ccGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATAc               <  1:207545/150‑1 (MQ=255)                                                                                                                                 ggcggTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGa             <  1:295035/150‑1 (MQ=255)                                                                                                                                           aTCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCg   >  2:84472/1‑150 (MQ=255)                                                                                                                                            tCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGt  >  2:417451/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                GTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGAAGTCGGCGGTCTGGATGTTGCCGATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCAGTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGT  >  NC_002947/4978853‑4979141

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.