New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	15 (0.580)	7 (0.310)	6/114	1.3	32.6%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	16 (0.720)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

TTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAA  >  NC_000913/4542629‑4542755                                                              |                                                                  tttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGt                                                             <  1:619517/68‑1 (MQ=255)      tttAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcat                                                        <  1:839612‑M1/68‑12 (MQ=255)       ttAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                       <  1:154575/68‑1 (MQ=255)          aCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCat                                                    <  2:134267/68‑1 (MQ=255)           catatTGATAATAAAGTTAAAAAAACAAAAAAATACAAGAAAATTGGGGCCAttttgactcatagagg                                                   >  1:610149‑M1/3‑52 (MQ=255)           cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagagg                                                   <  2:44718‑M1/68‑17 (MQ=255)           cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                       <  2:644399/64‑1 (MQ=255)           cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                       >  1:644399/1‑64 (MQ=255)           cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCata                                                   >  1:584961/1‑68 (MQ=255)                tGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagc                                              >  1:640533‑M1/1‑47 (MQ=255)                  ataataAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATATATAAGt                                            <  1:219500/68‑1 (MQ=255)                                 aaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                             >  1:89776/1‑68 (MQ=255)                                     aaataaatACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                         <  2:972611/68‑1 (MQ=255)                                           ataCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagt                        >  1:722363‑M1/1‑20 (MQ=255)                                           ataCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagt                        <  2:722361‑M1/63‑44 (MQ=255)                                           ataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaa                   >  2:496853/1‑68 (MQ=255)                                             aCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAat                 >  2:447305/1‑68 (MQ=255)                                                  aCAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggc            <  2:348433‑M1/68‑56 (MQ=255)                                                  aCAATTGGGGCCAAACTGTCCATATCATAAATAAGt                                            >  2:972546/1‑36 (MQ=255)                                                  aCAATTGGGGCCAAACTGTCCATATCATAAATAAGt                                            <  1:972549/36‑1 (MQ=255)                                                  aCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaa            >  1:4328/1‑68 (MQ=255)                                                      ttGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaa        <  1:116841‑M1/68‑60 (MQ=255)                                                       tGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaat       <  1:701654‑M1/68‑61 (MQ=255)                                                       tGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaat       <  2:440474‑M1/68‑61 (MQ=255)                                                        ggggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACg      <  1:577793/68‑1 (MQ=255)                                                         gggCCAttttgactcatagaggatatcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:723343‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:410263‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:664330‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:198489‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:723342‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:718549‑M1/68‑63 (MQ=255)                                                         gggCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatat     <  1:66740‑M1/68‑63 (MQ=255)                                                          ggCCAttttgactcatagaggaaagcatcgcggccaaactttttcagtttatttgttggcttaatatt    >  2:210418‑M1/1‑5 (MQ=255)                                                            ccAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattct  <  2:300256‑M1/68‑66 (MQ=255)                                                              |                                                                  TTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAA  >  NC_000913/4542629‑4542755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.