New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4542606	48 (0.810)	11 (0.200)	11/272	5.0	17.7%	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	57 (1.020)					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.

TATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913_3_pae_tpiA/4542463‑4542754                                                                                                                                                |                                                                                                                                                     tataCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTg                                                                                                                                                 >  1:954956/1‑149 (MQ=255)     ccGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTcta                                                                                                                                             >  2:102844/1‑147 (MQ=255)      cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATCCAAGACAATTGTGGCCAAACTTTcact                                                                                                                                            >  2:214649/1‑146 (MQ=255)      cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTATCAat                                                                                                                                            >  2:117530/1‑149 (MQ=255)      cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTCGGGACAAACTGTCCat                                                                                                                                            >  1:674619/1‑149 (MQ=255)      cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAACTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTCAAAAAAACAAAAAAATACAAGACAAATGGAGCCAAACTGTCAat                                                                                                                                            >  1:584854/1‑149 (MQ=255)       gCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaaa                                                                                                                                                    <  2:566462/140‑1 (MQ=255)       gCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaaa                                                                                                                                                    >  1:566462/1‑140 (MQ=255)          aGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAGGGCCAAACTGTCCATATCa                                                                                                                                        >  1:676641/1‑149 (MQ=255)          aGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATAGAAAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCAAATCa                                                                                                                                        >  1:676610/1‑149 (MQ=255)                             ccGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCAAAACTGTCCATATCATAAATAAGTTACGTAtttt                                                                                                                     >  2:334707/1‑149 (MQ=255)                             caggATTATCGGATATAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAAAACGTAACGTAtttt                                                                                                                     >  2:271555/3‑149 (MQ=255)                               ggaggaTGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTAGTTAtttttt                                                                                                                   >  2:535415/6‑149 (MQ=255)                                      gggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGc                                                                                                            >  1:726127/1‑149 (MQ=255)                                           agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTATCAAGCATaaa                                                                                                       >  2:688040/1‑149 (MQ=255)                                             aaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAACACAAATAAATACAAAACAATTGGTGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTATCAAGCATaaaaa                                                                                                     >  2:465410/1‑149 (MQ=255)                                                   tctcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAAAAAATAAATACAAGACAATTGGGGCCAAACTTTCCATATCATAAATAAGATACGTATTTTTTCTCAAGAAGAAAAATATaaa                                                                                               >  1:364435/1‑149 (MQ=255)                                                          accGATAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGCCACTTGGGGCCAAACTGTCCATATCCTAAATAAGTTACGTATTTTTTCTCCAGCATAAACATATTTAAAAACgt                                                                                        <  2:805285/147‑2 (MQ=255)                                                                aaaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                                  <  2:869550/149‑1 (MQ=255)                                                                   ttAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTAACATATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAGGCa                                                                               >  1:267709/1‑149 (MQ=255)                                                                        aaaagatgatGTTTGAATTAACTTATAGATAATAAAGTTAAAAATACAAATAAATACAAGACAATTGGGGCCAATCTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTaa                                                                          <  2:833143/146‑1 (MQ=255)                                                                         agagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTCACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAc                                                                         <  1:685443/149‑1 (MQ=255)                                                                           agaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTg                                                                       >  1:357791/1‑149 (MQ=255)                                                                             aagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtt                                                                     >  1:747491/1‑149 (MQ=255)                                                                              agcagTTTGATATAACATATTGAAAAAAAAATAAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTTAAGCATAAAAATATTAAAAAACGAAAAAAAGCATCTAACTGttt                                                                    <  2:609495/145‑1 (MQ=255)                                                                              agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                                    <  1:564783/149‑1 (MQ=255)                                                                                  gTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                                <  2:395078/149‑1 (MQ=255)                                                                                   tttGATATAACTTATATAAAATAAAGTAAAAAAAACAAATAAATAAAAGACAATTGAGGCCAAACTGTTCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               <  1:102844/149‑1 (MQ=255)                                                                                        tttAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTaaa                                                          >  1:728353/1‑149 (MQ=255)                                                                                              ttATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAATTGTTTGATATGTAAATTAttt                                                    >  2:9577/1‑149 (MQ=255)                                                                                                 ttGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAAAATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTa                                                 >  1:868834/1‑149 (MQ=255)                                                                                                  tgaatataaATTTAAAAAGACAAATAAATACAAGCGAGGTGGGCGCAAACTGTCCATATCATAAATATGTCACGTATTTTCTTTCAAGCATTAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                                <  2:484004/144‑1 (MQ=255)                                                                                                   tataaaaAAGTTAAAAAAAAAAATAAATAAAAAACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                               <  1:130043/148‑1 (MQ=255)                                                                                                   gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAATCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                               >  2:816151/1‑149 (MQ=255)                                                                                                       ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaa                                           >  1:77611/1‑149 (MQ=255)                                                                                                         aaaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaat                                         >  1:897770/1‑149 (MQ=255)                                                                                                                aaaaaaCAAATAACGACAATACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAATGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  <  1:918078/149‑1 (MQ=255)                                                                                                                 aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATAAAAAAACGACAAAAAGCATCTAACTATTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                                 >  2:1023544/1‑149 (MQ=255)                                                                                                                      cAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTATTTGATCTGTAGATTATTTCTATTGTAAATTAATTTCACATCa                            >  1:922946/1‑149 (MQ=255)                                                                                                                       aaataaatAAAGAAAAATTGGGGTCAAACTGTACATATCAGAAATAAGTTACGTATTTCTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc                           <  2:209273/149‑1 (MQ=255)                                                                                                                         ataaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCTTCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCt                         <  1:986054/149‑1 (MQ=255)                                                                                                                           aaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACATcc                       >  2:838732/1‑149 (MQ=255)                                                                                                                                   gACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACAACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTACAATCACCACCGAtataat               >  2:444991/1‑147 (MQ=255)                                                                                                                                      atttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTTTAAATTAATTTCACATCACCTCCGCTATATGTaa            >  1:171631/3‑149 (MQ=255)                                                                                                                                      atttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATAATAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAAATATTTCTATTGTAAATAAATTTCACATCACCTCCGCTATATGTaa            >  1:109340/3‑149 (MQ=255)                                                                                                                                          ggggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACCGTACCTCACCTACATGTAAAGCt        >  2:520989/1‑149 (MQ=255)                                                                                                                                           gggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTTTAAATTAATTTCACATCACCTCCGCTTTATGTaaaatta       >  2:305929/1‑145 (MQ=255)                                                                                                                                                aaaCTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTACGCTATATGTAAAGCTAACGtt  >  1:15918/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                     TATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913_3_pae_tpiA/4542463‑4542754

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.