New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4957572	48 (0.910)	7 (0.150)	4/224	NT	14.1%	intergenic (‑55/+108)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein
	?	NC_002947	= 4957632	43 (0.920)					intergenic (‑115/+48)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein

GGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCGGTTTCCAC  >  NC_002947/4957487‑4957778                                                                                                                                                  |                                                                                                                                                   ggTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaac                                                                                                                                                 >  4:67606‑M2/1‑146 (MQ=255)  gTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacc                                                                                                                                                >  5:296547‑M2/1‑145 (MQ=255)     gCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgc                                                                                                                                             <  5:292008‑M2/149‑8 (MQ=255)           gtggtgTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTTGGCCGACACGGTCCCTTCTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGAGAAAACCAGCATTGCCAGGACCGACGCCTACGACGCTAaacccgctccta                                                                                                                                        <  4:336418‑M2/148‑13 (MQ=255)                        gtggGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCATGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCCGCGTc                                                                                                                          >  8:154680/1‑149 (MQ=255)                              aTGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTAt                                                                                                                    <  6:292008/149‑1 (MQ=255)                                    tCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATc                                                                                                              >  5:120338/1‑149 (MQ=255)                                      aTGGTCTCAAACCATGTTTGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATcgc                                                                                                            <  3:336418/149‑1 (MQ=255)                                       tGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCgg                                                                                                                        <  6:70624/136‑1 (MQ=255)                                       tGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCgg                                                                                                                        >  5:70624/1‑136 (MQ=255)                                        gTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATcgcg                                                                                                           >  5:42941/1‑148 (MQ=255)                                         ttCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGaa                                                                                                         <  8:63350/149‑1 (MQ=255)                                         ttCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGaa                                                                                                         >  5:16235/1‑149 (MQ=255)                                             cAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATAcc                                                                                                     >  8:304765/1‑149 (MQ=255)                                              aaaCCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATcgc                                                                                                            <  8:63023/141‑1 (MQ=255)                                              aaaCCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATcgc                                                                                                            >  7:63023/1‑141 (MQ=255)                                              aaaCCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATAc                                                                                                      <  6:42941/147‑1 (MQ=255)                                              aaaCCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCt                                                                                                    <  7:304765/149‑1 (MQ=255)                                                       tCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCAt                                                                                            <  1:210336/148‑1 (MQ=255)                                                        cGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCAtt                                                                                           <  6:16235/148‑1 (MQ=255)                                                          gCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTc                                                                                         >  8:137311/1‑148 (MQ=255)                                                              acacGGTCCCTTGTAGGAGCGGGTTCACCCGCAAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCgg                                                                                    >  6:123065/1‑149 (MQ=255)                                                                        ttGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCtt                                                                             >  2:24372/1‑146 (MQ=255)                                                                        ttGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCtt                                                                             <  1:24372/146‑1 (MQ=255)                                                                                gCGGGTTCACCCTCGAATGCTTCGGCATCTACATCCTAGATTGCCAGGACCGAGGCCTTCTCTGGTAAACCCTCTCCTACAAAAGGCGGCGGCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCa                                                                  <  7:154680/149‑1 (MQ=255)                                                                                gCGGCTTCACCCGCGAATTCGTCGGCACCGACAACCTCCATAGCCAGGACCGACGCCTTCGCGGGAAAACCCGCTCCTACAAAAGCCGGAATCGGCTATGGGATCGCGAATACATTAGATCATATCATCGGAGCCCTTGCCCCCCAGCa                                                                  >  8:205956/1‑149 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtctgccgaacatggtt                                                                                                            >  8:329731‑M2/1‑57 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtcggccgaacatggtttgagaacatgacagcatgcccaccaaagaac                                                                             <  4:330726‑M2/128‑72 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtcggccgaacatggtttgagaacatgacagcatgcccaccaaagaac                                                                             >  3:330726‑M2/1‑57 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtcggccgaacatggtttgagaacatgacagcatgcacaccaaagaac                                                                             <  8:99235‑M2/128‑72 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtcggccgaacatggtttgagaacatgacagcatgcacaccaaagaac                                                                             >  7:99235‑M2/1‑57 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAaacccgctcctacaagggaccgtgtcggccgaacatggtt                                                                                                            <  7:329731‑M2/97‑41 (MQ=255)                                                                                          ccGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGcc                                                        >  5:345179/1‑149 (MQ=255)                                                                                           cgcgAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCg                                                       <  7:137311/149‑1 (MQ=255)                                                                                              gAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGAtc                                                             >  5:331594/1‑140 (MQ=255)                                                                                              gAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGAtc                                                             <  6:331594/140‑1 (MQ=255)                                                                                                aTGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATggg                                                                                                                 >  6:274771/1‑86 (MQ=255)                                                                                                aTGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATggg                                                                                                                 <  5:274771/86‑1 (MQ=255)                                                                                                aTGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCATTCGCGGGTGaacccgctcctacaagggaccgtgtcggccgaacatggtttgagaacatgacagcatgcccaccaaagaacaccaccccagcgacctgatccgtgccc                                                  <  2:346777‑M2/149‑99 (MQ=255)                                                                                                                aaCCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCa                                                                                             <  5:55217/90‑1 (MQ=255)                                                                                                                aaCCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCa                                                                                             >  6:55217/1‑90 (MQ=255)                                                                                                                  ccTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGCGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAAt                                >  6:225986/1‑149 (MQ=255)                                                                                                                  ccTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAAt                                <  5:123065/149‑1 (MQ=255)                                                                                                                   cTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATg                               <  7:47025/149‑1 (MQ=255)                                                                                                                       aTTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGa                           <  6:345179/149‑1 (MQ=255)                                                                                                                          gCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGa                        >  2:204803/1‑149 (MQ=255)                                                                                                                                 ccGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGAtttcttt                 <  1:204803/149‑1 (MQ=255)                                                                                                                                   gACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATttctttct               >  4:330615/1‑149 (MQ=255)                                                                                                                                    aCGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGcc                                                        <  4:11986/107‑1 (MQ=255)                                                                                                                                    aCGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGcc                                                        >  3:11986/1‑107 (MQ=255)                                                                                                                                        cTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCg                                      <  4:214910/121‑1 (MQ=255)                                                                                                                                        cTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCg                                      >  3:214910/1‑121 (MQ=255)                                                                                                                                        cTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGcgcg          >  1:88563/1‑149 (MQ=255)                                                                                                                                         ttCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCgg         >  3:73612/1‑149 (MQ=255)                                                                                                                                              gggTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCGGTTTc     >  1:58606/1‑148 (MQ=255)                                                                                                                                              gggTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCGGTTTc     >  5:280456/1‑148 (MQ=255)                                                                                                                                                gTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCGGTTTCCAc  >  4:76130/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                   GGTCGCTGGGGTGGTGTTCTTTGGTGGGCATGCTGTCATGTTCTCAAACCATGTTCGGCCGACACGGTCCCTTGTAGGAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGCACGATCTCGCCGGCCTCGGCCATGCGCCGGGCAATGGTGAGGATTTCTTTCTGCGCGGTTTCCAC  >  NC_002947/4957487‑4957778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.