New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4542606	26 (0.880)	4 (0.140)	4/272	3.5	13.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_tpiA	= 4542902	26 (0.940)					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.

AGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAAC  >  NC_000913_3_pae_tpiA/4542472‑4542751                                                                                                                                       |                                                                                                                                                  aGTAATGCTGCTAGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCa                                                                                                                                     >  1:194250/1‑149 (MQ=255)  gTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCat                                                                                                                                    >  1:261320/1‑149 (MQ=255)   aacggctgctTCTTTTGTCTGATAATGGGAAAGAAATAATATCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTGAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCata                                                                                                                                   <  2:207818/145‑1 (MQ=255)      tgctgcTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaat                                                                                                                                <  1:319700/149‑1 (MQ=255)          gctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGt                                                                                                                            <  1:366867/149‑1 (MQ=255)           ctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATAACATAAATAAGtt                                                                                                                           >  1:2597/1‑149 (MQ=255)            tCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTa                                                                                                                          <  1:126620/149‑1 (MQ=255)                             gggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                                                                                                         >  2:426554/1‑149 (MQ=255)                                  agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTTATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaa                                                                                                    <  2:399587/149‑1 (MQ=255)                                            tcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATACATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                          >  1:127164/1‑149 (MQ=255)                                               tAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                       <  1:264534/149‑1 (MQ=255)                                               tAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                       <  2:107257/149‑1 (MQ=255)                                                 aaCGAAAAATTAAAAAGAGAAACGGTTTGATTTAACTTACTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGTGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGa                                                                                     <  1:414734/149‑1 (MQ=255)                                                 aaCAAAAAAATAAAAGGAGAAGAGGTTTGATTTAAATTATTGATAATAAAATTAAAAAAACAAATAAATACAAGACAATTGGAGCCAAACTCACCAAATCATAAATAAGTTACGTATTTTTTATCAAGCATAAAAATTTAAAGAAACGa                                                                                     >  2:179749/1‑149 (MQ=255)                                                    gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaa                                                                                  >  1:56927/1‑149 (MQ=255)                                                              aaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAAGACACAAAGAGTCTa                                                                        >  2:162116/1‑149 (MQ=255)                                                                   gaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACACTTGGGGCCCAACTGTCCATAGCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGAACAAAATCATCTaaattt                                                                   >  2:84071/1‑145 (MQ=255)                                                                     agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                                 <  1:403512/149‑1 (MQ=255)                                                                     aactgTTTCATTTAACTGAAGGAAAATAAAGTTAAAAAAACAAATAAATACAAGACAAATGTGGCCAAACCGTCCATATCATAAATAAGCTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                                 <  2:285785/145‑1 (MQ=255)                                                                         gTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                             >  1:307011/1‑149 (MQ=255)                                                                                            taaataaGTTAAAAAAACAAATAAATACAAGACTATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAGTTTTTCTAAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                          <  2:155034/144‑1 (MQ=255)                                                                                                              aaataaatACAAGACAATTGGGGACAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACATAATGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc                        <  1:232176/149‑1 (MQ=255)                                                                                                                        aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAATCGACAAAAAGCATCTAACTTTTTGATATCTAAATTATTTCTATTATAAATAAATATCACATCACCTCCTCtaaa              >  1:500720/1‑147 (MQ=255)                                                                                                                          ggacgtgggggCCAAACTGGTCAAAGCATAAAAAAGTTAGTTATTTTTTCTTGAGCATAAAAATATTAAAAAAAAAAAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATg            <  2:202721/142‑1 (MQ=255)                                                                                                                               ttGGGGCCAAAATGGCCATAAAGTAAATAAGTTATGTATTTTTTTTCAAGTATAAAAATATTAAAAAAAGACAACAAGCAACTAACTTGTTGATAGGTAAATTATTTCTATTGTAAATTATTTTCACATCACCTCCGCTATATGTAAAg       <  2:206962/149‑1 (MQ=255)                                                                                                                                    gCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTTTTATTTTTAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATTTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCTCTATATATAAACCTAAc  >  2:300706/1‑149 (MQ=255)                                                                                                                                       |                                                                                                                                                  AGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAAC  >  NC_000913_3_pae_tpiA/4542472‑4542751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.