New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	12 (0.380)	13 (0.450)	9/216	1.3	49.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	15 (0.520)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

TCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAA  >  NC_000913/4542868‑4543119                                                                                                                                 |                                                                                                                            tgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCt                                                                                                                   >  2:247117‑M2/129‑139 (MQ=255)        aaaaaCCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgggg                                                                                                            <  1:260445/139‑1 (MQ=255)               accTCATGCAATATCAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGATTGTCCGCGATGCTTTCCTCTATGAGCCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACt                                                                                                     >  1:386889/1‑139 (MQ=255)                 aatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgt                                                                                                   <  1:124386‑M2/27‑1 (MQ=255)                                  tCTAAAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCGCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCaa                                                                                  >  1:379845/1‑139 (MQ=255)                                    tataAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAc                                                                                >  1:481315/1‑139 (MQ=255)                                     caaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACt                                                                               >  1:606316‑M2/93‑139 (MQ=255)                                               gctgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGATTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaa                                                                     >  2:413318‑M2/83‑139 (MQ=255)                                               aTAACAATTGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaa                                                                     <  2:386889/139‑1 (MQ=255)                                               aTAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaa                                                                     <  2:481315/139‑1 (MQ=255)                                                 tgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaac                                                                   <  2:49444‑M2/59‑1 (MQ=255)                                                    aaTAGAATATTAAGCCAACAAATACACTGAAAAAGTTTGTCCGCGATGCTTTACTCTATGAGTCAAAATGGCCCCAGATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacaaa                                                                <  1:453391/139‑1 (MQ=255)                                                              tAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgggg                                                                                                            <  2:61635/85‑1 (MQ=255)                                                              tAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgggg                                                                                                            >  1:61635/1‑85 (MQ=255)                                                                          ttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgt                                                                                                   >  1:623311‑M2/56‑82 (MQ=255)                                                                          ttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgt                                                                                                   <  2:623311‑M2/27‑1 (MQ=255)                                                                                 tgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGAttt                                   <  1:174804‑M2/91‑1 (MQ=255)                                                                                         tGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                  <  2:240716/68‑1 (MQ=255)                                                                                         tGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                  >  1:240716/1‑68 (MQ=255)                                                                                                            atatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAagcag        >  2:259073‑M2/22‑139 (MQ=255)                                                                                                              tGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAgcagca      >  2:257492/1‑139 (MQ=255)                                                                                                               tggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttttt                     >  2:177529‑M2/19‑123 (MQ=255)                                                                                                               tggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttttt                     >  2:301098‑M2/19‑123 (MQ=255)                                                                                                               tggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttttt                     <  1:301098‑M2/105‑1 (MQ=255)                                                                                                               tggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttttt                     <  1:177529‑M2/105‑1 (MQ=255)                                                                                                                aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGa                                                   >  1:498116/1‑92 (MQ=255)                                                                                                                aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGa                                                   <  2:498116/92‑1 (MQ=255)                                                                                                                  tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGaa  >  1:489219/1‑139 (MQ=255)                                                                                                                           ccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACATAACAAAGTGTACAGAAGGAc                                                  <  1:432289‑M2/76‑1 (MQ=255)                                                                                                                           ccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGAc                                                  >  2:432289‑M2/7‑82 (MQ=255)                                                                                                                           ccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtt                         >  2:29630‑M2/7‑107 (MQ=255)                                                                                                                           ccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtt                         <  1:29630‑M2/101‑1 (MQ=255)                                                                                                                                 |                                                                                                                            TCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAA  >  NC_000913/4542868‑4543119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ 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.