New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4542598 =	29 (0.740)	7 (0.190)	6/262	3.8	18.1%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_tpiA	4542912 =	36 (0.980)					intergenic (+363/‑119)	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.

ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAA  >  NC_000913_3_pae_tpiA/4542454‑4542745                                                                                                                                                 |                                                                                                                                                    aCTGGGCGTAATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTAGGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTggg                                                                                                                                                 <  2:224566/149‑1 (MQ=255)   tgtgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAGGGc                                                                                                                                               >  1:385259/1‑149 (MQ=255)     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)                                                                                                                                                 |                                                                                                                                                    ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAA  >  NC_000913_3_pae_tpiA/4542454‑4542745

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.