New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 454260643 (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.

TTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  NC_000913_3_pae_tpiA/4542462‑4542754
                                                                                                                                                |                                                                                                                                                     
ttATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACt                                                                                                                                                   <  1:547065/149‑1 (MQ=255)
                 ctgctCGTTTTGCCGTATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                                                                                 <  1:94246/149‑1 (MQ=255)
                 ctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                                                                                 <  2:691213/149‑1 (MQ=255)
                     tCGTTTTGACAGATTAAGAGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTCGGGCCAAACTGTCCATATCATAAATAAGTTa                                                                                                                             <  2:489607/149‑1 (MQ=255)
                                  tgacgggAAAGAAATAATCTCATAAACGAAAAAATAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAACCACAGTCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                                <  1:569110/145‑1 (MQ=255)
                                       ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                           >  1:131187/1‑149 (MQ=255)
                                       ggAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                           >  2:620747/1‑149 (MQ=255)
                                        gaaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATGGAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCAt                                                                                                          >  1:356374/1‑149 (MQ=255)
                                         aaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTAATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGAATa                                                                                                         >  2:207706/1‑149 (MQ=255)
                                             aaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaaa                                                                                                     >  2:63515/1‑149 (MQ=255)
                                                     tcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                             >  1:570559/1‑149 (MQ=255)
                                                       aTAAACGGAAAATTAAAAAGAGAAGAGGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                           <  2:703053/149‑1 (MQ=255)
                                                        tAAACGAAAAATTAAAAATAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                          <  2:57394/149‑1 (MQ=255)
                                                         aaaCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAAAAAAGTAAAAAAAAACAATAAATACAAAACAATTAGGTAAAAACTGTCCAAATCATAAATAAGATAACTAGTGATTATTCAGCATAAGACGATTaaaaagca                                                                                         >  2:391633/1‑146 (MQ=255)
                                                          aaCGAAAAATGAAACAGAGGAGGTGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGTGCCAAACTGTCTATATCATAAATTAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGa                                                                                        <  2:298129/149‑1 (MQ=255)
                                                                 aaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAg                                                                                 <  1:267856/149‑1 (MQ=255)
                                                                     aaaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATACCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATc                                                                             <  1:63515/149‑1 (MQ=255)
                                                                      aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAGACATcg                                                                            >  1:311986/1‑148 (MQ=255)
                                                                                          tAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt                                                        >  2:291899/1‑149 (MQ=255)
                                                                                                  tGATAATAAAGTTAAAAAAACAAATAAATTCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                                <  1:620747/149‑1 (MQ=255)
                                                                                                    ataataAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTg                                              >  2:168494/1‑149 (MQ=255)
                                                                                                    acaaaaaaGGTAAAAAAACAAAGAAATTCATTATTATATGAGTCTACCTGTACATAACATGAATAAGTTACGTATTTTTCGCTAAGTCTAAAAATATTAACAATAGACATAAGGCATCTGACTGTTTGATATGTAAATTATTCCTATTg                                              <  2:388170/144‑1 (MQ=255)
                                                                                                        taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                          <  2:131187/149‑1 (MQ=255)
                                                                                                        taaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                          >  1:417896/1‑149 (MQ=255)
                                                                                                         aaaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATTAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaat                                         <  1:168494/149‑1 (MQ=255)
                                                                                                          aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               <  1:460205/126‑1 (MQ=255)
                                                                                                          aaGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGatat                                                               >  2:460205/1‑126 (MQ=255)
                                                                                                            gaaaaaaaaaaaaATAAATACAAGACAATTGGGGCCAAATTGTCCATATCATAAATAAGTTACGTATTCTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaa                                      <  2:311986/146‑1 (MQ=255)
                                                                                                            gTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATAACATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTTAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAaattaa                                      <  1:207706/149‑1 (MQ=255)
                                                                                                            gTTAAAAAAAAAAATAAATACCAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTTTAaatgaa                                      <  2:487387/149‑1 (MQ=255)
                                                                                                                 aaaaaaaaATAAATATAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTGTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                                 <  2:499664/149‑1 (MQ=255)
                                                                                                                    aaCAAATAAATGCAAGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAATCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACAt                              <  2:266133/149‑1 (MQ=255)
                                                                                                                          taaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTc                        >  1:85520/1‑149 (MQ=255)
                                                                                                                                 aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCgata                 >  1:51666/1‑149 (MQ=255)
                                                                                                                                  aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat                >  1:375718/1‑149 (MQ=255)
                                                                                                                                  aGACAAGTGGGGCTAAACGTCGCATTTTATAAATAAGGTAAGTAGTTTGTCTAGAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat                <  2:581943/149‑1 (MQ=255)
                                                                                                                                   gACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  >  2:593230/1‑130 (MQ=255)
                                                                                                                                   gACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                  <  1:593230/130‑1 (MQ=255)
                                                                                                                                      aaTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaa            >  2:353391/1‑149 (MQ=255)
                                                                                                                                       aTTGGGGCCAAACTGTCCATATCATAAAGAAGTGACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaaa           <  2:615818/149‑1 (MQ=255)
                                                                                                                                         gggggGCAAACAGTCTATATTATAAAGAAGTTAGGGATTTTTTGTGAAGGATAATAATATTAAAAAACGACAAAGAGCCTCTAACTGCTTGATATGTAATTTTTTTCTATTGTAAATTAATTTCATATGACCTCGGCTTTATGTAAAGc         <  2:548731/148‑1 (MQ=255)
                                                                                                                                           gggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTCTATGTACAGCTa       >  1:560499/1‑149 (MQ=255)
                                                                                                                                                aaaCTGTCCATATCATAAATAAGTTACGTATTTTTTTTTTTTCTTTAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTAATATGTAAATTATTTCTATTGTAGATTAATTTCACATCACCTCCGCTATATGTAAAGTTAATGtt  >  2:41347/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                                     
TTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  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.