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

CTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGTCC  >  NC_002947/4978803‑4979098                                                                                                                                                      |                                                                                                                                                      cTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATGTCAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGa                                                                                                                                                       <  1:107006/149‑1 (MQ=255)         cgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGaca                                                                                                                                                     >  8:275368‑M1/102‑143 (MQ=255)         cgacggccagatcgtcactgacaacggctacgccctggagcctgccattgtcgtgcctaacgacgcgcagaccttcaccgttggccaggacggcaccgtgtC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGaca                                                                                                                                                     <  7:275368‑M1/42‑1 (MQ=255)                         cACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGt                                                                                                                               >  5:342439/1‑148 (MQ=255)                              gcggcgGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAg                                                                                                                           <  1:139133/147‑1 (MQ=255)                              gcggcgGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAg                                                                                                                           <  8:5596/147‑1 (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‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGa                                                                <  4:276977/148‑1 (MQ=255)                                                                                                        tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAg                                               <  6:98724/149‑1 (MQ=255)                                                                                                        tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAg                                               <  6:352616/149‑1 (MQ=255)                                                                                                        tGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGACAACGGTGAAGGTCTGCGCGTCGTTAGGAACGACAAGGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAg                                               >  2:117217/1‑149 (MQ=255)                                                                                                         gTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                                                                     <  3:6191/127‑1 (MQ=255)                                                                                                         gTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCa                                                                     >  4:6191/1‑127 (MQ=255)                                                                                                            tgtcgatcaccaccgccggcaacccggctgcacaggtgatcgACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCg                                                  >  8:275368‑M2/43‑143 (MQ=255)                                                                                                            tgtcgatcaccaccgccggcaacccggctgcacaggtgatcgACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCg                                                  <  7:275368‑M2/101‑1 (MQ=255)                                                                                                                gatcaccaccgccggcaacccggctgcacaggtgatcgACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGATCAGGt                                        >  8:16074‑M2/39‑149 (MQ=255)                                                                                                                 atcaccaccgccggcaacccggctgcacaggtgatcgACACGCTGCCGTCCTGCACAACGGTCAAGCTCTGCGCGTCGTGAGGCACGACAATGGCAGGCTCCAGGGCGAAGCCGTTATCA‑GTGACGATCATGCCGTCGCAGAAcaggag                                       >  4:56803‑M2/38‑147 (MQ=255)                                                                                                                    ACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGaa                                    >  5:91561‑M1/1‑149 (MQ=255)                                                                                                                     ccaccgccggcaacccggctgcacaggtgatcgACACGGTGCCGTCCTGCCCAACGGTGAAGGTCGGCGCGTCGTTAGGCACGGCAATGGCAGGGTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTGAGGTGGAAg                                   >  2:99611‑M2/34‑149 (MQ=255)                                                                                                                      CTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAgg                                  <  3:1423‑M1/149‑1 (MQ=255)                                                                                                                               cGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCAc                         >  2:92164/1‑149 (MQ=255)                                                                                                                                        ggcggTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCACGTGACGATCTGGCCGTCGGAGTTCATGTGGAAGGTACCGTCACGGGTATAc                 <  1:92164/149‑1 (MQ=255)                                                                                                                                         gcggTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGa               <  2:35928/149‑1 (MQ=255)                                                                                                                                               gtgatcgACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGt         <  6:167380‑M2/142‑1 (MQ=255)                                                                                                                                                      acacGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGa                                                                <  2:5368/87‑1 (MQ=255)                                                                                                                                                      acacGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGa                                                                >  1:5368/1‑87 (MQ=255)                                                                                                                                                      acacGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGTcc  <  2:265040/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                      CTGGGGTGCCGACCTGAGGCGCGCCACTGGCGGCGGTCTCGAGGAACAGGTTGTCGCCGATCGCCTGCAGGCCGGCCGGGTTGATG‑AAGTCGGCGGTCTGGATGTTGCC‑GATCACCTGTGCAGCCGGGTTGCCGGCGGTGGTGATCGACACGGTGCCGTCCTGGCCAACGGTGAAGGTCTGCGCGTCGTTAGGCACGACAATGGCAGGCTCCAGGGCGTAGCCGTTGTCA‑GTGACGATCTGGCCGTCGGAGTTCAGGTGGAAGGTACCGTCACGGGTATACGACACGGTGCCGTCC  >  NC_002947/4978803‑4979098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.