New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1045234 =	23 (0.980)	11 (0.470)	9/270	NT	44.0%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	CP009273	= 1973123	5 (0.210)					intergenic (‑669/‑111)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

TGGTGCCAGTAGTACCCGTCGTTGCCTCGGTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATC  >  CP009273/1045086‑1045379                                                                                                                                                     |                                                                                                                                                  tggggCCAGTAGTACCCGTCGTTGCCTCGGTCCCGTTTGTTTCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACgg                                                                                                                                                   <  2:160881/149‑1 (MQ=255)     aagaaaggcaacaatcaacttaatgttaatgaaatgttttacatatattaaccacttgtttaatgcggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGa                                                                                                                                               >  2:416277‑M1/145‑149 (MQ=255)             caacaatcaacttaatgttaatgaaatgttttacatatattaaccacttgtttaatgcggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGGTGCCa                                                                                                                                       <  2:21085‑M1/13‑1 (MQ=255)                ccGTCGTTGCCTCGGTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAATTCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACt                                                                                                                                    >  2:317417/1‑149 (MQ=255)                  ctcgtTGGCTCGGTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTa                                                                                                                                  <  2:235489/148‑1 (MQ=255)                      ttGCCTCGGTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGa                                                                                                                              <  2:124537/149‑1 (MQ=255)                              ttaatgaaatgttttacatatattaaccacttgtttaatgcggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAgtgt                                                                                                                      <  2:308688‑M1/30‑1 (MQ=255)                              ggcccGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATTGACAATACGGGTGATGCTGCCAACTTACTGAtt                                                                                                                            <  1:219716/141‑1 (MQ=255)                              gTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGAtt                                                                                                                            <  1:186796/143‑1 (MQ=255)                                            ttCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTCGTGTATGATGGTGttttt                                                                                                        >  2:95739/1‑149 (MQ=255)                                               atatattaaccacttgtttaatgcggacaatgagtacgctattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACCTACTGATTTAGTGTATGATGGTGTTTTTGAg                                                                                                     >  2:303369‑M1/103‑149 (MQ=255)                                                    tagcaAACGCAGCTTGCGTCGTCAACATGAAGGCCATAAGGATTTCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGa                                                                                                      <  1:353315/142‑1 (MQ=255)                                                    gagcaAACGCAGCTTGCGTCGTCAACATGAAGGCCATCAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGCTCCTCCCCACTTCCTGATTTAGCGTACGCTGGTGTTTCTGa                                                                                                      <  1:145838/142‑1 (MQ=255)                                                       caAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCa                                                                                             >  2:77500/1‑149 (MQ=255)                                                            gCAGCTTGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGc                                                                                        <  2:229463/149‑1 (MQ=255)                                                              aGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTAGAGGTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCtt                                                                                      >  2:62417/1‑149 (MQ=255)                                                                ttaatgcggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTg                                                                                          <  1:286891‑M1/58‑1 (MQ=255)                                                                     gcggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGGGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTc                                                                               <  2:138592‑M1/69‑1 (MQ=255)                                                                     gcggagaatcagtacactattttcttataattacaattgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTc                                                                                     <  1:230020‑M1/63‑1 (MQ=255)                                                                      cggagaatcagtacactattttcttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCt                                                                                    <  1:323664‑M1/64‑1 (MQ=255)                                                                          cAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCa                                                                          <  2:78912/149‑1 (MQ=255)                                                                                     ccATAAGGATTGCAGAAAGCTTGTGGTTCATAACTTTTCCTTTATTCATCGCAGGGACAATACGGGTGATGCTGCCAACTTACTGAGTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                                                     <  1:333495/143‑1 (MQ=255)                                                                                             ttataattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGc                                                       <  2:270529‑M1/93‑1 (MQ=255)                                                                                             ttataattacatttgaaattatatgatcaacgggagggattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTATTTTTGAGGTTCTCCCGTGGCTTCTGTGTCTATCAGCTGTACATcccgtttcgc                                                       <  2:187098‑M1/93‑5 (MQ=255)                                                                                              ttGCAGAAAGCTTGTGTTTCAAAACTTTTCCTTTATTCATCGCATGGACAATAAGGGTGATGCTGCCAACTTCAAGAGTTAGTGTATGATTGTGGTTTTGAGGCTCTCCATTGGCTTCTGTTTCAATCAGCTGGCCCTCCTGt                                                            >  1:118017/1‑143 (MQ=255)                                                                                                taattacatttgaaattatatgatcaccgggagtgattgattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGTGGTTCTCCAGTGGCTTCTGTTTCTATCACCTGTCCCTCCTGTTCAGCTAc                                                    <  2:69942‑M1/96‑1 (MQ=255)                                                                                                    aaaGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCt                                                      >  1:343427/1‑143 (MQ=255)                                                                                                    aaaGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTGCTGAc                                                >  2:152469/1‑149 (MQ=255)                                                                                                         ttGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggt                                           >  2:367355/1‑149 (MQ=255)                                                                                                         atgtgTTTCATAACTTTTCCTTTATTCATCGGATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTGCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGa                                                 >  1:283061/2‑143 (MQ=255)                                                                                                                     aCTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGCCGGGGTGGTGct                                     >  1:293252/1‑142 (MQ=255)                                                                                                                     aCTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTGTTTGAGGTTCTCCACTGGCTTCTGTTTCTCTCAGCTGTCCCTCCTGTTCAGCTACTGACggggggtggcg                                     >  1:217427/1‑136 (MQ=18)                                                                                                                             tttATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCa                       >  2:41157/1‑149 (MQ=255)                                                                                                                                      gattaattatctttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTg                    <  1:301794‑M1/128‑1 (MQ=255)                                                                                                                                             aCAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTGACGGCACGAGAACCGCCGGACa             >  1:390198/1‑143 (MQ=11)                                                                                                                                               aaTACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTAGTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAgcgca     <  2:280006/149‑2 (MQ=37)                                                                                                                                                aTACGGGGGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCa          <  1:149511/143‑1 (MQ=25)                                                                                                                                                  ttaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTAtc  <  2:378616‑M1/146‑1 (MQ=255)                                                                                                                                                  aCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCtctc  >  2:17119/1‑149 (MQ=25)                                                                                                                                                  aCGGGTGATGCTGCCAACTTACTGATCTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAgc        <  1:84922/143‑1 (MQ=21)                                                                                                                                                    gggTGATGCTGCCGACTTACTGATTTAGTGTATGATGGTGTTCTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGAGGTCGTGCGTAACCGCTAAAGCACTGCCGGACACCGgcgc      >  1:267280/1‑143 (MQ=11)                                                                                                                                                     |                                                                                                                                                  TGGTGCCAGTAGTACCCGTCGTTGCCTCGGTCCCGTTTGTTGCTTCAGGGGCAGCAAACGCAGCTGGCGTCGTCAACATGAAGGCCATAAGGATTGCAGAAAGCTTGTGTTTCATAACTTTTCCTTTATTCATCGCATGGACAATACGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATC  >  CP009273/1045086‑1045379

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.