New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4542606	29 (0.600)	8 (0.180)	8/272	4.8	19.5%	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	39 (0.860)					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.

CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAG  >  NC_000913_3_pae_tpiA/4542460‑4542746                                                                                                                                                   |                                                                                                                                             cGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaaa                                                                                                                                            <  1:161535/149‑1 (MQ=255)         cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAGGGCCAAACTATCCat                                                                                                                                    >  2:622272/1‑149 (MQ=255)         cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAAATAAAAAGAGAAGACGATTGATTTAACTTCTAAATAATAAACATAAAAAAACAAATAAATACAACACAGTTCGAGCCAAACTGTccct                                                                                                                                    >  2:479924/1‑147 (MQ=255)               tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAAAGGTTTGATATAACTTATTGATAATAAAGCTAAAAAAACAAATAAATACAAGACAATTACGCCCAAACTGTCCATATCatc                                                                                                                              >  2:282782/1‑148 (MQ=255)                    ctgctCGTTTTACCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                                                                         >  1:534841/1‑149 (MQ=255)                             ttGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAt                                                                                                                <  2:534841/149‑1 (MQ=255)                                 cGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGCTTGATTTAACTTAATGATAATAAAGTTAAAAAAAAAAATAAATACAAGAGAATTGGGTCCAAACTATCCATATCATAAAAAAGTAACGTAtgttt                                                                                                            >  2:835133/1‑149 (MQ=255)                                       attggAAAGGAATAATATGATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                                                                                      <  2:433041/146‑1 (MQ=255)                                              agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaa                                                                                               >  1:695106/1‑149 (MQ=255)                                               gaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCAAAACTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCATaaaa                                                                                              >  2:581223/1‑149 (MQ=255)                                                          aTAAACCAAAAATTAAAAAAAAAAAAAGTTCCATCTAACTTACTGAAAATAAAGTAAAAAAAACAAATAAATACAAGACAATTCGGGCCAAACAGTCCATACAATAAATAAGTTACCTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                   <  2:773402/149‑1 (MQ=255)                                                            aaaCGAAAAATTAAAAAGAGAAGAGGGTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACg                                                                                 >  2:481862/1‑149 (MQ=255)                                                             aaCAAAAAATTAAAAAGATAAGTGTTTTGATTTAAATTAGTGCAAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTTTCCATATTATAAATAAGTTCCGTATTTTTTCTCAAGAATAAAAATATTAAAAAACGa                                                                                <  2:782658/149‑1 (MQ=255)                                                                          aaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAATGCATCTa                                                                   >  1:380017/1‑149 (MQ=255)                                                                           aagagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATAAAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATAAAAAAAACAAAAAAAGCacataa                                                                  >  2:360932/1‑144 (MQ=255)                                                                             gagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCCTATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACt                                                                <  1:647843/149‑1 (MQ=255)                                                                                      tttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                       >  1:549034/1‑149 (MQ=255)                                                                                      tttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                       >  1:238603/1‑149 (MQ=255)                                                                                        tGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTTTTTGATATGt                                                     >  2:36696/1‑149 (MQ=255)                                                                                          atatAACTTATTGATAATAAACTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTaa                                                   <  2:273094/146‑1 (MQ=255)                                                                                                     tGATAATAAATTTAAAAAAAAAAATAATTACATTAATATTGAGGACAAACTGTCTATTTCATAAATAATTTACGGATTTTTTCTCAAGCTTTAAAATTTAAAAAAAAAAAAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                        <  2:378344/149‑1 (MQ=255)                                                                                                     gtaaaataaAGTAAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                        <  2:759358/145‑1 (MQ=255)                                                                                                           taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                  >  1:524382/1‑149 (MQ=255)                                                                                                                 tAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaatt                            <  1:726774/149‑1 (MQ=255)                                                                                                                                ataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATACGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTCCTCTTGTAATTTAATTTCACATCACCTCCGc             >  1:17395/1‑149 (MQ=255)                                                                                                                                       aCAATTGGGCCCAAACTGTCCATATCACAAATAAGCTACGTATTTTTTCTCAAGCAAAAAAATATTAAAAAACGACAAAAAGCAACTAACTGTTTGATATATAAATTCTTTCTATTGTACATTAATTTCACATCCCCTCCGCtaccatt      >  2:707726/1‑144 (MQ=255)                                                                                                                                        cAATTGGGGCCAAACTGTCCATATCATAAATTAGTTACGTATTTGTTATCAAGCATAAAAATATTAAAAAACGACAAACAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAATTTAAGTTGATATCACCTCCGCTACATGTa     <  2:522698/149‑1 (MQ=255)                                                                                                                                           ttGGGGCCAAACTGTCCATATCAAAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAg  <  1:256133/149‑1 (MQ=255)                                                                                                                                           ttGGCGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCGTAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAg  <  2:805366/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                             CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAG  >  NC_000913_3_pae_tpiA/4542460‑4542746

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.