New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4542606	43 (1.040)	5 (0.130)	5/268	5.0	10.3%	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	47 (1.210)					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.

TTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913_3_pae_tpiA/4542462‑4542754                                                                                                                                                 |                                                                                                                                                      ttATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACt                                                                                                                                                   <  1:547065/149‑1 (MQ=255)                  ctgctCGTTTTGCCGTATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCataaataa                                                                                                                                 <  1:94246/149‑1 (MQ=255)                  ctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCataaataa                                                                                                                                 <  2:691213/149‑1 (MQ=255)                      tCGTTTTGACAGATTAAGAGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTCGGGCCAAACTGTC‑CATATCATAAATAAGTTa                                                                                                                             <  2:489607/149‑1 (MQ=255)                                   tgacgggAAAGAAATAATCTCATAAACGAAAAAATAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAACCACAGTCAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTtctc                                                                                                                <  1:569110/145‑1 (MQ=255)                                        ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                           >  1:131187/1‑149 (MQ=255)                                        ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                           >  2:620747/1‑149 (MQ=255)                                         gaaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATGGAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCAt                                                                                                          >  1:356374/1‑149 (MQ=255)                                          aaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTAATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑AATATCATAAATAAGTTACGTATTTTTTCTCAAGAATa                                                                                                         >  2:207706/1‑149 (MQ=255)                                              aaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                                                                                     >  2:63515/1‑149 (MQ=255)                                                      tcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                             >  1:570559/1‑149 (MQ=255)                                                        aTAAACGGAAAATTAAAAAGAGAAGAGGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                           <  2:703053/149‑1 (MQ=255)                                                         tAAACGAAAAATTAAAAATAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                          <  2:57394/149‑1 (MQ=255)                                                          aaaCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAAAAAAGTAAAAAAAAACAATAAATACAAAACAATTAGGTAAAAACTGTC‑CAAATCATAAATAAGATAACTAGTGATTATTCAGCATAAGACGATTaaaaagca                                                                                         >  2:391633/1‑146 (MQ=255)                                                           aaCGAAAAATGAAACAGAGGAGGTGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGTGCCAAACTGTC‑TATATCATAAATTAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGa                                                                                        <  2:298129/149‑1 (MQ=255)                                                                  aaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAg                                                                                 <  1:267856/149‑1 (MQ=255)                                                                      aaaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATACCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATc                                                                             <  1:63515/149‑1 (MQ=255)                                                                       aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAGACATcg                                                                            >  1:311986/1‑148 (MQ=255)                                                                                           tAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt                                                        >  2:291899/1‑149 (MQ=255)                                                                                                   tGATAATAAAGTTAAAAAAACAAATAAATTCAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                                <  1:620747/149‑1 (MQ=255)                                                                                                     ataataAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTg                                              >  2:168494/1‑149 (MQ=255)                                                                                                     acaaaaaaGGTAAAAAAACAAAGAAATTCATTATTATATGAGTCTACCTGTA‑CATAACATGAATAAGTTACGTATTTTTCGCTAAGTCTAAAAATATTAACAATAGACATAAGGCATCTGACTGTTTGATATGTAAATTATTCCTATTg                                              <  2:388170/144‑1 (MQ=255)                                                                                                         taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                          <  2:131187/149‑1 (MQ=255)                                                                                                         taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                          >  1:417896/1‑149 (MQ=255)                                                                                                          aaaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATTAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaat                                         <  1:168494/149‑1 (MQ=255)                                                                                                           aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               <  1:460205/126‑1 (MQ=255)                                                                                                           aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               >  2:460205/1‑126 (MQ=255)                                                                                                             gaaaaaaaaaaaaATAAATACAAGACAATTGGGGCCAAATTGTC‑CATATCATAAATAAGTTACGTATTCTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaa                                      <  2:311986/146‑1 (MQ=255)                                                                                                             gTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATAACATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTTAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaa                                      <  1:207706/149‑1 (MQ=255)                                                                                                             gTTAAAAAAAAAAATAAATACCAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTTTAaatgaa                                      <  2:487387/149‑1 (MQ=255)                                                                                                                  aaaaaaaaATAAATATAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTGTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                                 <  2:499664/149‑1 (MQ=255)                                                                                                                     aaCAAATAAATGCAAGACAATTGGGGCCAAACTGTC‑AATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAATCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACAt                              <  2:266133/149‑1 (MQ=255)                                                                                                                           taaataCAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTc                        >  1:85520/1‑149 (MQ=255)                                                                                                                                  aaGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCgata                 >  1:51666/1‑149 (MQ=255)                                                                                                                                   aGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat                >  1:375718/1‑149 (MQ=255)                                                                                                                                   aGACAAGTGGGGCTAAAC‑GTCGCATTTTATAAATAAGGTAAGTAGTTTGTCTAGAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat                <  2:581943/149‑1 (MQ=255)                                                                                                                                    gACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  >  2:593230/1‑130 (MQ=255)                                                                                                                                    gACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  <  1:593230/130‑1 (MQ=255)                                                                                                                                       aaTTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaa            >  2:353391/1‑149 (MQ=255)                                                                                                                                        aTTGGGGCCAAACTGTC‑CATATCATAAAGAAGTGACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaaa           <  2:615818/149‑1 (MQ=255)                                                                                                                                          gggggGCAAACAGTC‑TATATTATAAAGAAGTTAGGGATTTTTTGTGAAGGATAATAATATTAAAAAACGACAAAGAGCCTCTAACTGCTTGATATGTAATTTTTTTCTATTGTAAATTAATTTCATATGACCTCGGCTTTATGTAAAGc         <  2:548731/148‑1 (MQ=255)                                                                                                                                            gggCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTCTATGTACAGCTa       >  1:560499/1‑149 (MQ=255)                                                                                                                                                 aaaCTGTC‑CATATCATAAATAAGTTACGTATTTTTTTTTTTTCTTTAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTAATATGTAAATTATTTCTATTGTAGATTAATTTCACATCACCTCCGCTATATGTAAAGTTAATGtt  >  2:41347/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                      TTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTC‑CATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913_3_pae_tpiA/4542462‑4542754

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.