New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2019533 =	36 (0.610)	3 (0.050)	3/268	NT	7.7%	intergenic (+20/‑85)	fliK/fliL	flagellar hook‑length control protein/flagellar biosynthesis protein
	?	NC_000913	2019576 =	37 (0.640)					intergenic (+63/‑42)	fliK/fliL	flagellar hook‑length control protein/flagellar biosynthesis protein

CGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACAGCTACTG  >  NC_000913/2019428‑2019721                                                                                                                                                     |                                                                                                                                                  gaataccagaatcgggatccaaagcgatcgcttgcttttcttgcttatcgcgtaatcagtcatgtgttgcggtcttcctgtgtcgccactgcttatcggctaattATCCGCGTCTTTTCCCCGCGTTGTTGCGCTCAAGACGCAGGATa                                                                                                                                                   >  1:970351‑M1/106‑149 (MQ=255)  gggggACGACGACGATACGCTTCCGGTTCCCATCTCTATACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTATCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATaa                                                                                                                                                  <  1:320998/149‑1 (MQ=255)   ggggTAGCCGACGATACGCTTCCGGTTCGCATCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAAt                                                                                                                                                 <  2:171850/149‑1 (MQ=255)       aaGACGACGATACGCTTCCGGTTCCCATCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGc                                                                                                                                             <  2:812670/149‑1 (MQ=255)         gacgacGATACGCTTCCGGGTCCCATCTCTTTACAAGGGCGAGTAACAGGCAACAGCGGCGGTGATAATTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCGACGATTTGTTGAGCTCAAGACGCAGTATAATTAGcag                                                                                                                                           >  1:492564/1‑147 (MQ=255)           cgacgaTACGCTTCCGGTTCCCATCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGAt                                                                                                                                         <  1:321661/149‑1 (MQ=255)            gacgaTACGCTTCCGGTTCCCATCTCTTTACAAGGGCGTGTAACATGCAACAGCGGCGTTGATATTTTCGCCTAACGACAGAGGTAGCACCGAAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGAGAATTAGCCGATa                                                                                                                                        >  1:581510/1‑149 (MQ=255)                    gCTTCCGGTTCCCATCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCAGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAg                                                                                                                                >  1:897709/1‑149 (MQ=255)                          ggTTCCCATCTC‑TTACAAGGGCGTGTAACAGGCAACAGCGGCGATGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGAGCTCAAGACGCAGGATAATTATGCGATAAGCAGTAGCGAcaca                                                                                                                         >  1:362402/1‑149 (MQ=255)                              cccATCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTATTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGACGATAATCAGTAGCGACACAGGa                                                                                                                      >  1:184183/1‑149 (MQ=255)                                 atctcTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGa                                                                                                                   >  1:450205/2‑149 (MQ=255)                                   ctctTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAACCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGAcc                                                                                                                 <  2:353717/149‑1 (MQ=255)                                     ctTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGACTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGc                                                                                                               >  1:227049/1‑149 (MQ=255)                                          cAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAacac                                                                                                          <  2:547291/149‑1 (MQ=255)                                                      aCAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGAATGATTaa                                                                                              >  1:979690/1‑148 (MQ=255)                                                       aaGGCAACAGCGGAGTTGATATTTTCGCCTTACGTCATAGGTAGCACCGTAATCCGCGTCTTTTCCGCGCTTTGTTGCGCTAAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACTGGAAGACCGCTACACATGACTGATTAcg                                                                                             <  2:184183/148‑1 (MQ=255)                                                          gCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGGCTGTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCATCACATGACTGATTAcgcgt                                                                                          >  2:988214/1‑148 (MQ=255)                                                                  ggcgTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGGGTTTTCCCGGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACTTGAGTGATTACGCGATAAgaatg                                                                                  >  2:257282/1‑145 (MQ=255)                                                                      ttGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGaaaa                                                                              <  2:1016585/149‑1 (MQ=255)                                                                       tGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAATCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAaag                                                                             >  2:389681/1‑149 (MQ=255)                                                                                         tCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGCCCGCAACACATGACTGATTACGCGATCAGCAAGAAAAGCAAGCGATCGCTGTGGAt                                                           >  1:713579/1‑149 (MQ=255)                                                                                         gcAGAGGTAGCAACGTCAGCCGCGTCGTTTCCCCGCGTTGTTGCGCTCAAGACGCTGGATAATTAGCCGTTAAGCAGTAGCGACTCAGGTATACCGCAACACATGACTGATTACGCGATAAGCATGAAAAGCAAGCGAGCGCTTTGGAt                                                           <  2:789165/148‑1 (MQ=255)                                                                                            gagGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGTTccc                                                        >  1:763361/1‑149 (MQ=255)                                                                                             agGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCg                                                       >  1:243745/1‑149 (MQ=255)                                                                                             agGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGACGATAAGCAGTAGCGACACAGGAAGACCGCATCCCATGACTGATTACGCGATAAGAAAGAAAAGCAAGCGATCGCTTTGGATACCg                                                       >  2:762007/1‑149 (MQ=255)                                                                                               gTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGAt                                                     >  2:35461/1‑149 (MQ=255)                                                                                                   cACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTg                                                 <  2:504266/149‑1 (MQ=255)                                                                                                    aCCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTgg                                                >  2:371909/1‑149 (MQ=255)                                                                                                      cGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATTATTAGCAGCTAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGAAAGCGATCGGTTTGGATCTCGATTCTGGtt                                              >  2:485245/1‑148 (MQ=255)                                                                                                       ttatTCCGAGTCTTTTCACAGCTTTGTTGCGCTCAAGTCTCAGGATAATTAGCCTATTATCAGTAGCGACACAGGAAGACCTCAACTCATGACTGATTACGCGATAATCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTAt                                             >  2:979690‑M1/5‑149 (MQ=255)                                                                                                         tatcctgcgtcttgagcgcaacaacgcggggaaaagacgcggatAATTAGCCGATAAGCAGTGGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTc                                           >  1:970351‑M2/45‑149 (MQ=255)                                                                                                          atcctgcgtcttgagcgcaacaaagcggggaaaagacgcggatAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCa                                          >  2:599591‑M2/44‑149 (MQ=255)                                                                                                          ATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCa                                          <  2:355304‑M1/149‑1 (MQ=255)                                                                                                           tcctgcgtcttgagcgcaacaaagcggggaaaagacgcggatAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCAt                                         <  1:599591‑M2/107‑1 (MQ=255)                                                                                                             CGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTa                                       <  1:929405‑M1/149‑1 (MQ=255)                                                                                                              gcgTCGTTTCCCAGCTTTGTTGCGCTCAAGACGGATGATAATTAGCCGATAAGCAGTCGCGACACAGGAAGACCGCAACACATGACTGCTTACGCCATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTAc                                      <  2:478830/149‑1 (MQ=255)                                                                                                                    tttCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTcgc                                >  1:518797/1‑149 (MQ=255)                                                                                                                         ccGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCt                           >  1:49224/1‑149 (MQ=255)                                                                                                                          cGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTGTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCtg                          >  2:502381/1‑149 (MQ=255)                                                                                                                           gCTTTGTTGCTCTCATGACCGAGGATAATTATCAGATAAGCATTAGCGACACAGGAAGACCGCAACACATGACTGATTCCGCGAAAAGCAAGAAAAGCCAGCGATCTCTTTGGAGCCCGATTCTGGTATTCATTCACCTCGCGGCCtgt                         <  2:492564/149‑1 (MQ=255)                                                                                                                              ttgttgCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGcc                      <  2:450205/149‑1 (MQ=255)                                                                                                                                    cgcTCAAGACGCAGGATAATTAGCCGAAAAGCAGTAGAGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCa                <  1:623535/149‑1 (MQ=255)                                                                                                                                         aaGACGCAGGATAATTAGCCGATAAGCAGTAGTGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTa           >  1:27728/1‑149 (MQ=255)                                                                                                                                         aaGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACCGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTATGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAggatc           >  1:580792/1‑146 (MQ=255)                                                                                                                                         aaGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTTTTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTa           >  2:952822/1‑149 (MQ=255)                                                                                                                                           gACGCAGGATAATTAGCCGATTAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACa         <  1:257282/149‑1 (MQ=255)                                                                                                                                            aCGCAGGATAAATAGCCGATAAGCAGTAGCGACACAGGAAGACCGCACCACCTGACTGATTACGCGATAAGCAAGAAACGCAAGCGATCGCTGTGGATCCCGATTCTGGTATTCAATACCCTCTCGGCATGTGCCAGCGCAGGtgtcag        >  2:662128/1‑144 (MQ=255)                                                                                                                                               cAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACAGCTa     >  1:432361/1‑149 (MQ=255)                                                                                                                                                  gatAATTAGCCGATAAGCAGTAGCGAGACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACAGCTACTg  <  2:897709‑M2/146‑1 (MQ=255)                                                                                                                                                  gatAATTAGCCGATAAGCAGTAGCGACACAGGATGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTAGGATCCCGCTTCTGGTATTCATTACCCTCGCGGCCTGTGCCCGCGCAGGTTACCGCGACTg  >  2:772917‑M2/4‑149 (MQ=255)                                                                                                                                                  gatAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACAGCTACTg  >  2:142644‑M2/4‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGCCGATAAGCAGTAGCGACACAGGAAGACCGCAACACATGACTGATTACGCGATAAGCAAGAAAAGCAAGCGATCGCTTTGGATCCCGATTCTGGTATTCATTACCCTCGCGGCCTGTGCCAGCGCAGGTTACAGCTACTG  >  NC_000913/2019428‑2019721

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.