New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4542606	25 (0.640)	6 (0.160)	6/262	3.8	16.8%	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	36 (0.980)					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.

TGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGC  >  NC_000913_3_pae_tpiA/4542458‑4542747                                                                                                                                                     |                                                                                                                                              tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCa                                                                                                                                               >  2:423018/1‑149 (MQ=255) tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCa                                                                                                                                               >  2:302342/1‑149 (MQ=255) tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCa                                                                                                                                               >  2:70516/1‑149 (MQ=255)        taCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTc                                                                                                                                        <  1:423018/149‑1 (MQ=255)              cAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATc                                                                                                                                  >  2:533341/1‑149 (MQ=255)                       tgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGCTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCTATATCATAATTAAg                                                                                                                         >  1:663405/1‑149 (MQ=255)                          tCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTa                                                                                                                      <  1:533341/149‑1 (MQ=255)                                    ggAATAAGGAAAAGAAATAAACGCATAAACAAAAAAAAAAAAATAGAAGAGGTTTGATTTAATTTATTGATAAAAAAAAAAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttttt                                                                                                            <  2:515066/149‑1 (MQ=255)                                                             tAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                   >  1:562168/1‑149 (MQ=255)                                                                  gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTATAAAGCATAAAAATATTAAAAAACGACaa                                                                              >  2:308603/1‑149 (MQ=255)                                                                     aaaTTAAATAGACAAGATGTTTAATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGGCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTTCGGATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                           <  2:665190/149‑1 (MQ=255)                                                                     aaaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                           <  1:350771/149‑1 (MQ=255)                                                                        ttAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCa                                                                        >  2:181023/1‑149 (MQ=255)                                                                         tAAAAAGAGTAGAGGTTTGCTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt                                                                       <  1:247134/149‑1 (MQ=255)                                                                         tAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt                                                                       <  1:594503/149‑1 (MQ=255)                                                                                   agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                             <  1:103360/149‑1 (MQ=255)                                                                                    gagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATACGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTg                                                            >  2:95588/1‑149 (MQ=255)                                                                                      agTTTGATATAACTTAAAAAAAAAAAAAATAAAAAAACAAATAAATACAAGACAATCGGGGCCAAACTGTCCATATCATAAATAATTTACGTATTTTTTTTCAAGCATAAAAATATTAAAAAAAAAAAAAAAGCATCTAACTGTTTGat                                                          <  2:34619/148‑1 (MQ=255)                                                                                             tttAACTTATGGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGATAAAAAGAATCTAACTGTTTGATATTTaac                                                   >  2:692220/1‑148 (MQ=255)                                                                                                                 ggtAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAACATCTAACTGTTTGATATGTAAATTATTTCTATTGtaaataaa                               >  2:64975/3‑149 (MQ=255)                                                                                                                      aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                          <  1:264624/149‑1 (MQ=255)                                                                                                                                      aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCtata          >  1:659078/1‑149 (MQ=255)                                                                                                                                       aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat         <  2:562168/149‑1 (MQ=255)                                                                                                                                       aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat         <  1:181023/149‑1 (MQ=255)                                                                                                                                        gACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATg        >  2:441254/1‑149 (MQ=255)                                                                                                                                           aaTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATTTTAAAAAACGACGAAAAGCATCTAACTGTTTGATATGTAAATTATTTTTATTGTAAATTAATTTCACATAAGCGCCGCTATATGtca     >  1:96417/1‑147 (MQ=255)                                                                                                                                            aTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaaa    <  1:30811/149‑1 (MQ=255)                                                                                                                                              tGGGTCCAAACTGTCCATATCATAAATAAGTTATGTACTTTTTCTAAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGc  <  2:385259/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                              TGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGC  >  NC_000913_3_pae_tpiA/4542458‑4542747

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.