New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4542598 =	40 (0.620)	8 (0.130)	7/264	7.2	15.6%	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 =	49 (0.810)					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.

ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATAT  >  NC_000913_3_pae_tpiA/4542454‑4542740                                                                                                                                                 |                                                                                                                                               aCTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTggg                                                                                                                                            <  1:660263/149‑1 (MQ=255)   tgtgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATATTAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGc                                                                                                                                          <  1:451132/149‑1 (MQ=255)     tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCa                                                                                                                                        >  2:102656/1‑149 (MQ=255)     tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAAAAAATAAATACAAGCAAATTGTGGCCa                                                                                                                                        >  2:102675/1‑149 (MQ=255)       cGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAATAAAAAACAAAAAAATTGGGGCCaaa                                                                                                                                      >  1:626002/1‑149 (MQ=255)        gTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGc                                                                                                                                          >  1:256431/1‑144 (MQ=255)        gTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGc                                                                                                                                          <  2:256431/144‑1 (MQ=255)        gTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAAc                                                                                                                                     >  1:173635/1‑149 (MQ=255)         ttAAACCGCGAGTAAGGATGATAGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCatttt                                                                                                                                    <  2:1119870/149‑5 (MQ=255)           ataCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGt                                                                                                                                  >  1:514269/1‑149 (MQ=255)              ccGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAAACAATTGCAGCCAAACTGTACa                                                                                                                               >  2:566728/1‑149 (MQ=255)                 ccAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                                                                                            >  1:82754/1‑149 (MQ=255)                     tAATGCTGTTCGTTTTGACGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCata                                                                                                                        <  1:566728/149‑1 (MQ=255)                         gctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGATCCAAACTGTCCATATCataaaaa                                                                                                                    >  1:505091/1‑147 (MQ=255)                                      ccGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttt                                                                                                       >  2:136513/1‑149 (MQ=255)                                      ccGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttt                                                                                                       >  2:319123/1‑149 (MQ=255)                                            tATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGATTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCCTATCATAAATAAGTAAAGTATTTTTtctaa                                                                                                 >  2:70142/1‑147 (MQ=255)                                              tGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATGTAACTTATTAATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTCAGTATTTTTTCTAAAg                                                                                               >  2:93865/1‑149 (MQ=255)                                              tGGGAAAGAAATAATCTCATAAACAAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACACAATAGTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAg                                                                                               <  1:792284/149‑1 (MQ=255)                                                  aaagaaaTAATCTCATAAAAGAAAAATTAAAAAGAGAAGAGGATAGATTTAAATTATTGATCATAACGTTAAAAAAACAAATAAAAACAAGACAATTGGGGCCAAACTGTCCATATCATAAATACGGGAGGTATTATTTCTCAAGGATa                                                                                           >  1:241031/1‑149 (MQ=255)                                                                 tAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                            <  1:136513/149‑1 (MQ=255)                                                                      gAAAAATGAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATATATACAAGACAATTGGGGCCAAACTGTCCCTATCATACATAAGTCACGTATTATTTCTCAAGCGTACAAAAATTAAAAAACGACaa                                                                       >  2:266999/1‑149 (MQ=255)                                                                         aaaTGAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAAAAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACaaaaa                                                                    <  2:997396/149‑1 (MQ=255)                                                                               aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt                                                              >  2:1043523/1‑149 (MQ=255)                                                                                           gTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                  <  1:917158/149‑1 (MQ=255)                                                                                              tGATTTAACTTATTGAGAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGTGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGt                                               >  1:109043/1‑149 (MQ=255)                                                                                                aTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                                                                              >  1:666918/1‑84 (MQ=255)                                                                                                aTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                                                                              <  2:666918/84‑1 (MQ=255)                                                                                                     aCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattat                                        >  1:704329/1‑149 (MQ=255)                                                                                                      cTTATTAAAAAAAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGACAAACTCTCCATATCATAAATAAGTTACGTTTTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattatt                                       <  1:102675/149‑1 (MQ=255)                                                                                                      cTTATAAATAATAAAATTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAattatt                                       <  1:102656/149‑1 (MQ=255)                                                                                                         aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCt                                    >  1:1086212/1‑149 (MQ=255)                                                                                                                        aaaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAAttt                     <  1:580445/149‑1 (MQ=255)                                                                                                                           aaaaCAAATAAATACAAGAAAAGGGGGGCCAAACTGTCCATATCATAAATAAGTTAAGTATTTTTTCTCAAGCATAAAAATATTAAAAAAAAAAAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcac                  <  2:394087/149‑1 (MQ=255)                                                                                                                            aaaCAAATAAATAAATGACAGTTGAGACCGAACTTTATATATCATATGTGATTTATGGATTTTTTCTTAAGTATAAAAATATTAAAAAACGACAAAAAGCATCTTACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcaca                 <  2:470060/149‑1 (MQ=255)                                                                                                                                    aaataTAATACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTcc         <  2:658839/149‑1 (MQ=255)                                                                                                                                          aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtct                                                                                                   <  2:626891/53‑1 (MQ=255)                                                                                                                                          aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtct                                                                                                   >  1:626891/1‑53 (MQ=255)                                                                                                                                          aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc             >  1:120545/1‑139 (MQ=255)                                                                                                                                          aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc             <  2:120545/139‑1 (MQ=255)                                                                                                                                           aaaCATTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGTATATAAATATTAAATAACGACTAAAAGTATTTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat  <  1:419157/147‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                               ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATAT  >  NC_000913_3_pae_tpiA/4542454‑4542740

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.