New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4541950	29 (0.530)	6 (0.120)	6/264	6.5	14.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_pgi	= 4542246	44 (0.850)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGT  >  NC_000913_3_pae_pgi/4541804‑4542086                                                                                                                                                   |                                                                                                                                         cGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAAGTAAAAAGAGAAGAGTTGTGATTTAACTTATTGATAATAAAGTTTAAAAAACAAATAAATACAATACAATTGAGACCaaa                                                                                                                                        >  1:449263/1‑149 (MQ=255)     aaaCCGCAAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGt                                                                                                                                    <  1:2432/147‑1 (MQ=255)      taCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTc                                                                                                                                   <  2:87453/149‑1 (MQ=255)               tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAAAACAAGACAATTGGGGCCAAACTGTCCATATCata                                                                                                                          >  1:666787/1‑149 (MQ=255)                    ctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                                                                     <  2:429199/149‑1 (MQ=255)                                  ggAATATGGGAAAGAAATAATATTAAAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttttt                                                                                                       <  2:775087/149‑1 (MQ=255)                                       aTGGGAAAGAAGTAATGTTATAAAAAAAAAATAAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                                                                                  <  2:709955/149‑1 (MQ=255)                                         gggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTGACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                                                                                                >  1:638153/1‑149 (MQ=255)                                         ggcaaagaaaTAAGCTCATAAACGCAAAAGTGGAAAGGTCAGAGGTTTGTTTGTACGTATAGAAAAAAAAAAAAAAAAAACAAAGAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                                                                                                <  2:205513/146‑1 (MQ=255)                                                  ataatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTTAATTTTaaaaaaa                                                                                       >  2:233759/1‑147 (MQ=255)                                                       ctccgaaaCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaa                                                                                  <  1:751712/144‑1 (MQ=255)                                                               cGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACa                                                                          >  2:685123/1‑149 (MQ=255)                                                                gAATAATCAAAAAGAGAAGACGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTTCCCATATCATAAATAAGTTAAGTATTTTTTCTAAAGCTTAAAATTATTAAAAAACGACaa                                                                         >  2:892979/1‑149 (MQ=255)                                                                gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGaaaa                                                                         >  1:584562/1‑149 (MQ=255)                                                                   aaaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                      >  1:566504/1‑149 (MQ=255)                                                                         aaaaGAGTAGGGGTGTGTTTTAGCTTATTGGTAATGAAGTTAAAAAAAGAAATAAATACAAGACAATTGGGGCGAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCATGTATAAAAATATTATAAAAGGACAAAAAGCATCt                                                                >  2:750665/1‑149 (MQ=255)                                                                                   aagTTAGAATTAAATTATTGATAATAAAGATAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAAAAAGTTACGTATTTTTTCTAAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa                                                      <  2:93563/147‑1 (MQ=255)                                                                                            ttAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAat                                             >  2:950305/1‑149 (MQ=255)                                                                                                 ttATTGATCATAAAGTTAAAAAAACAAATAAATGCAAGACAATTCGGGACAAACTCTCCATATCATAAAAAAGTTACGTATTTTTACTCAAAAATAAAAATCTTAAAAAACAACAAAAAGCAAATAACTATTTAATATGTaaaacagtt                                        >  2:662200/1‑143 (MQ=255)                                                                                                  aaTTGATAATAAAATTAAAAAAAAAAATAAATACAAGATAATTGGCGACAAACTGTCCATATCATAAATAAGTTACGTATTTTTGCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTc                                       <  2:153680/148‑1 (MQ=255)                                                                                                     tGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                    <  1:778794/149‑1 (MQ=255)                                                                                                      caaaataaAGTTAAAAAAACAAATAAATACCAGACAAGTGGGGACAAACTGCCCATATCATTACTAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                   <  1:744551/146‑1 (MQ=255)                                                                                                                   aaaaaaCAAATAAATACAAGACAATTCGGGCCAAACTATCCATATCATACAAAAGTTACGTATTTTTTCTCAACCATAAAAATATTAAAAAACGACAAAAAGCCTCAACCTGTTTGCTCTCTAAATTATTTCTTTTCTAAATTAAttta                      >  2:216039/1‑148 (MQ=255)                                                                                                                    aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                     <  2:638153/149‑1 (MQ=255)                                                                                                                                  aCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                        <  2:836077/116‑1 (MQ=255)                                                                                                                                  aCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                        >  1:836077/1‑116 (MQ=255)                                                                                                                                    aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                     >  2:299751/1‑133 (MQ=255)                                                                                                                                    aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                     <  1:299751/133‑1 (MQ=255)                                                                                                                                       aCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCtattttt  >  2:745390/1‑145 (MQ=255)                                                                                                                                                   |                                                                                                                                         CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGT  >  NC_000913_3_pae_pgi/4541804‑4542086

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.