New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4541950	18 (0.460)	6 (0.160)	6/264	4.2	19.1%	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	34 (0.920)					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.

CGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAG  >  NC_000913_3_pae_pgi/4541812‑4542090                                                                                                                                           |                                                                                                                                              cGCCAGTAATGCTGCTCGGTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAATTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCat                                                                                                                                     >  1:592216/1‑149 (MQ=255)              gctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCAGAAAGGAAAAATTAAAAAGAGAAGAGGCTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGt                                                                                                                        >  1:194417/1‑149 (MQ=255)                                        aaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAAAAAATAAATACAAGACAATTGGGGCCAAACTGTACATATCATAAATAAGTTACGTATTTTTTCTCAACCAT‑acaaa                                                                                             >  2:505113/1‑149 (MQ=255)                                                        gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACaa                                                                             >  1:342400/1‑149 (MQ=255)                                                                              tttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                       >  1:405860/1‑149 (MQ=255)                                                                                  aTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTaa                                                   <  2:182827/149‑1 (MQ=255)                                                                                       aCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattat                                              >  1:278869/1‑149 (MQ=255)                                                                                         taataaataataAAATTAAAAAAAAAAATAAATACAAGAAAATAGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAAAAACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                            <  2:683239/143‑1 (MQ=255)                                                                                          attggATAATAAAGTTAAAAAGATTAATAAATACAAGACAATTGGGGACAAACTGGCAATTTCATACCTATGTCACGTATTTTTTCTCTAGTATAAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                            <  2:251231/145‑1 (MQ=255)                                                                                             tGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                        >  1:326210/1‑149 (MQ=255)                                                                                              gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                       >  1:38620/1‑149 (MQ=255)                                                                                                 aataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTa                                    <  1:397154/149‑1 (MQ=255)                                                                                                             aaaaCAAATAAATACAAGACAATGGGGGCCAAAGTGTCCATATTATAAATCAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcac                        <  1:68683/149‑1 (MQ=255)                                                                                                              aaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcaca                       >  1:102630/1‑149 (MQ=255)                                                                                                                  aaataaatACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTAAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTATATTGTAAATTAATTTCACATCaa                   >  2:387407/1‑148 (MQ=255)                                                                                                                    ataaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCt                 >  1:411862/1‑149 (MQ=255)                                                                                                                        ataCAAGATAATCGGGGCCAAACTGGCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGGCAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGc             <  1:125541/149‑1 (MQ=255)                                                                                                                                   ttGGGGCCAAACTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAg  <  1:2504/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                              CGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAT‑AAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAG  >  NC_000913_3_pae_pgi/4541812‑4542090

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.