New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	16 (0.130)	3 (0.030)	3/280	12.5	4.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	108 (0.920)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
Rejected: Position hash score below cutoff.

AGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATAT  >  NC_000913/4542506‑4542777                                                                                                                                                                                 |                                                                                                aGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAAc                                                                                      <  4:373873/188‑1 (MQ=255)                                      gCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAACAAACAAATAAATACAAGACACtt                                                                                                >  3:457202/1‑141 (MQ=255)                                                        tgctgcTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaata                                                                     <  2:391663/150‑1 (MQ=255)                                                                         gATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat  <  4:380088/200‑1 (MQ=255)                                                                                                                                                    aGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                      >  2:569172/1‑57 (MQ=255)                                                                                                                                                    aGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                      <  4:569237/57‑1 (MQ=255)                                                                                                                                                                 aataaataCAAGACAATTGGGGCCAAACTGTCCATATCataaata                                                                     >  2:639852/1‑45 (MQ=255)                                                                                                                                                                 aataaataCAAGACAATTGGGGCCAAACTGTCCATATCataaata                                                                     <  4:639917/45‑1 (MQ=255)                                                                                                                                                                 aataaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                        <  1:411795/74‑1 (MQ=255)                                                                                                                                                                 aataaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                        >  3:411811/1‑74 (MQ=255)                                                                                                                                                                      ataCAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                      >  2:469814/1‑39 (MQ=255)                                                                                                                                                                      ataCAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                      <  4:469855/39‑1 (MQ=255)                                                                                                                                                                      ataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAc            <  1:374348/97‑1 (MQ=255)                                                                                                                                                                      ataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAc            >  3:374362/1‑97 (MQ=255)                                                                                                                                                                           aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                        <  2:278699/64‑1 (MQ=255)                                                                                                                                                                           aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                        >  4:278710/1‑64 (MQ=255)                                                                                                                                                                                 |                                                                                                AGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATAT  >  NC_000913/4542506‑4542777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.