New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4960665 =	39 (0.700)	3 (0.060)	3/242	NT	7.2%	coding (154/333 nt)	fliE	flagellar hook‑basal body complex protein FliE
	?	NC_002947	4960707 =	40 (0.760)					coding (112/333 nt)	fliE	flagellar hook‑basal body complex protein FliE

GCCTGGACCAGCTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGG  >  NC_002947/4960517‑4960813                                                                                                                                                     |                                                                                                                                                     gCCTGGACCAGCTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATg                                                                                                                                                      <  2:264829/149‑1 (MQ=255)   cTGGACCAGCTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATg                                                                                                                                                      >  8:105578/1‑147 (MQ=255)   cTGGACCAGCTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATg                                                                                                                                                      <  7:105578/147‑1 (MQ=255)     aaaaaaatgcggccgcaggagagagaagggtcatgagccaaggtgttgaattcaatcgtctgatgttggacatgcgggccatgcaggccgatgccatgtcgctgcccaaggtaactgccgcccccgagctggcgccagggcaaaGCAcc                                                                                                                                                  <  4:212703‑M1/5‑1 (MQ=255)     aaaaaaatgcggccgcaggagagagaagggtcatgagccaaggtgttgaattcaatcgtctgatgttggacatgcgggccatgcaggccgatgccatgtcgctgcccaaggtaactgccgcccccgagctggcgccagggcaaaGCAcc                                                                                                                                                  <  7:216291‑M1/5‑1 (MQ=255)            cTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGa                                                                                                                                           >  3:267619/1‑149 (MQ=255)               gttgCGTACCTGTGTCATGGCTTGGATCGACACGCTGGCCTGTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGAt                                                                                                                                          <  6:21150/147‑1 (MQ=255)                ttgCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGAtggc                                                                                                                                       <  3:133850/149‑1 (MQ=255)                   cGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGAtggcctg                                                                                                                                    >  5:202752/1‑149 (MQ=255)                                              acGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTg                                                                                                         >  2:202515/1‑149 (MQ=255)                                               gtgttgaattcaatcgtctgatgttggacatgcgggccatgcaggccgatgccatgtcgctgcccaaggtaactgccgcccccgagctggcgccagggcaaaGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGc                                                                                                        >  6:312154‑M1/103‑149 (MQ=255)                                                gCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGcc                                                                                                       >  7:30099/1‑149 (MQ=255)                                                 cTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGccc                                                                                                      <  4:267619/149‑1 (MQ=255)                                                    gCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCt                                                                                                     <  7:256517/147‑1 (MQ=255)                                                           gCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAg                                                                                             >  4:33456/1‑148 (MQ=255)                                                            cGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGAGAAGGTGCTTTGCCCTGGCTCCAGCt                                                                                           >  7:261120/1‑149 (MQ=255)                                                             gAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGAtggcctgg                                                                                                                                   <  6:345242/108‑1 (MQ=255)                                                             gAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGAtggcctgg                                                                                                                                   >  5:345242/1‑108 (MQ=255)                                                                  gATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGACTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                     >  2:261375/1‑149 (MQ=255)                                                                           gtcagtcaGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGtt                                                                             >  4:100330/1‑148 (MQ=255)                                                                               gtcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCtt                                                                        <  6:202752/149‑1 (MQ=255)                                                                                tcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                     >  4:121435/1‑135 (MQ=255)                                                                                tcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                     <  3:121435/135‑1 (MQ=255)                                                                                gcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTg                                                                       <  3:100330/148‑1 (MQ=255)                                                                                    gTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTggg                                                                     >  5:224689/1‑147 (MQ=255)                                                                                        aCGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGa                                                               <  5:307102/149‑1 (MQ=255)                                                                                         cgccgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGAc                                                              <  8:30099/149‑1 (MQ=255)                                                                                            cgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATg                                                           >  8:207511/1‑149 (MQ=255)                                                                                            cgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGCGGCGGCAGTTACCTTGGGCAGCGACATg                                                           <  1:202515/149‑1 (MQ=255)                                                                                                 ttGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATc                                                      >  2:108608/1‑149 (MQ=255)                                                                                                   gCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCAt                                                       <  3:33456/146‑1 (MQ=255)                                                                                                   gCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCgg                                                    >  3:131758/1‑149 (MQ=255)                                                                                                     cGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGc                                                   >  8:159181/1‑148 (MQ=255)                                                                                                     cGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGc                                                   <  7:159181/148‑1 (MQ=255)                                                                                                            gAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATgg                                           <  3:310588/149‑1 (MQ=255)                                                                                                            gAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATg                                            <  1:108608/148‑1 (MQ=255)                                                                                                             cccaaggtaactgccgcccccgagctggcgccagggcaaaGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAg                                                                                                                 <  4:14780‑M1/38‑1 (MQ=255)                                                                                                             cccaaggtaactgccgcccccgagctggcgccagggcaaaGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAg                                                                                                                 >  3:14780‑M1/41‑78 (MQ=255)                                                                                                                               gTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAg                        <  7:207511/149‑1 (MQ=255)                                                                                                                                tCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGa                       >  8:316939/1‑149 (MQ=255)                                                                                                                                   agtcTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCACTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGa                    >  8:194456/4‑149 (MQ=255)                                                                                                                                   aGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCt                                                 >  8:153756/1‑120 (MQ=255)                                                                                                                                   aGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCt                                                 <  7:153756/120‑1 (MQ=255)                                                                                                                                     gCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGAtt                  <  7:316939/149‑1 (MQ=255)                                                                                                                                       ttGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGAc                      >  3:267322/1‑143 (MQ=255)                                                                                                                                       ttGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGAc                      <  4:267322/143‑1 (MQ=255)                                                                                                                                          ctgcGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCATTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAAtt             >  2:207415/1‑149 (MQ=255)                                                                                                                                                   aTGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCATACGATTGAATTCAACACCtt    >  2:265267/1‑149 (MQ=255)                                                                                                                                                   aTGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCtt    <  6:224689/149‑1 (MQ=255)                                                                                                                                                     GCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTgg  <  6:345692‑M1/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     GCCTGGACCAGCTTGTTGCGTACCTGGGTCATGGCTTGCATCGACACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGG  >  NC_002947/4960517‑4960813

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.