New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	37 (1.090)	4 (0.130)	4/246	NT	11.7%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	26 (0.820)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

CTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAA  >  NC_000913/4542860‑4543136                                                                                                                                         |                                                                                                                                             cTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACAGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTAAAAATGACCCCAAATGTTTc                                                                                                                                        >  2:537604/1‑143 (MQ=255)   cATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCAt                                                                                                                                      >  1:573252/1‑143 (MQ=255)     ttcttcTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAACGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAATTGtcttgtat                                                                                                                                    >  1:412119/1‑136 (MQ=255)     ttcttcTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAATTGtcttgtat                                                                                                                                    >  2:492791/1‑136 (MQ=255)         tctctcCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTg                                                                                                                                <  2:352845/143‑1 (MQ=255)          ctctcCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgg                                                                                                                               >  1:500734/1‑143 (MQ=255)           tctcCAAAAACCACCTCATGCAATATAAACATCGATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTggg                                                                                                                              <  1:585037/143‑1 (MQ=255)               cAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaa                                                                                                                          >  1:32859/1‑143 (MQ=255)                 agaaCCTCCGCATGCAACATACACATCTATACACAAAGATAACAATAGAATATTAAGCCAACAAATAACCTGAAAAAGTTTGTCCGCGATGCTCTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaaa                                                                                                                        <  1:20725/141‑1 (MQ=255)                   aaCCACCTCATGCGATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACt                                                                                                                      <  2:254469/143‑1 (MQ=255)                      caccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                                   >  1:643993/1‑143 (MQ=255)                      caccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCCTTAGGGGGAACACtgtg                                                                                                                   >  2:21200/1‑143 (MQ=255)                          atagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAgt                                                                                                               >  2:575910‑M2/112‑143 (MQ=255)                             tGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGtt                                                                                                            <  1:368099/143‑1 (MQ=255)                               aataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTgg                                                                                                          >  1:653293‑M2/107‑143 (MQ=255)                                  tataAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAg                                                                                                       >  1:171307/1‑143 (MQ=255)                                             ataaataaAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGtt                                                                                            <  2:175317/143‑1 (MQ=255)                                             ataaataaAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGtt                                                                                            <  2:157513/143‑1 (MQ=255)                                                 caggtagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTaca                                                                                        <  1:663295‑M2/55‑1 (MQ=255)                                                   aaaGATAACTATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAACATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaa                                                                                      <  2:117119/143‑1 (MQ=255)                                                             aTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGCTGCCTTCCTCTACGCGTCAAAATGGCCCCAAATGTTTCATCTTTTGGCAGAAACCGGTGCAGCGTTGGCAGTCACACTCGTTTGCACCACACAGCGTa                                                                            >  2:108569/1‑143 (MQ=255)                                                               aGAATATTAAGCCAACAAATAATCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACa                                                                          <  1:214114/143‑1 (MQ=255)                                                                    atTAAGCCAACAAACAACCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTGGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACg                                                                     <  1:63183/143‑1 (MQ=255)                                                                     ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGCACGa                                                                    >  1:646946/1‑143 (MQ=255)                                                                         ttaatatttttatgcttgacaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGc                                                                <  2:562993‑M2/79‑1 (MQ=255)                                                                                           aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAAt                                              >  1:202689/1‑143 (MQ=255)                                                                                            aaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAACCAAAGAGTACAGAACGACTTTCAATGTCGATTCAGAAATa                                             >  2:3318/1‑143 (MQ=255)                                                                                                     cgcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACACAGTGTACAGAACGACTGCCCATGTCGAGTGAGAAACAGTTTATTga                                    >  1:632999/1‑143 (MQ=255)                                                                                                           gCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaaggaa                              >  1:579005/1‑143 (MQ=255)                                                                                                                  tctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAgcagca                       >  2:282379/1‑143 (MQ=255)                                                                                                                     aTGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGGCCAGAACGACGGCCCATGTCGCTTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGa                    >  2:511088/1‑143 (MQ=255)                                                                                                                          tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGACTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAACAtt               >  2:265664/1‑143 (MQ=255)                                                                                                                            aaaaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTaa             >  2:462167/1‑143 (MQ=255)                                                                                                                            aaaaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTaa             >  1:352966/1‑143 (MQ=255)                                                                                                                                       aaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTACAACTCTGGCaa  >  2:100021‑M2/3‑143 (MQ=255)                                                                                                                                         |                                                                                                                                             CTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAA  >  NC_000913/4542860‑4543136

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.