New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4542598 =	19 (0.520)	5 (0.150)	5/268	4.3	18.9%	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 =	25 (0.730)					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.

GCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTT  >  NC_000913_3_pae_tpiA/4542768‑4543057                                                                                                                                                 |                                                                                                                                                  gaaTCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCTCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGtt                                                                                                                                               <  2:620664/147‑1 (MQ=255)            aTTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgg                                                                                                                                    <  2:351577/149‑1 (MQ=255)                     tcCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACt                                                                                                                           >  2:218263/1‑149 (MQ=255)                       cAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGCATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAAtgt                                                                                                                         >  1:256204/1‑149 (MQ=255)                       cAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTATCATCCTTTGAGGGAAAACtgt                                                                                                                         >  1:377434/1‑149 (MQ=255)                              caccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtgt                                                                                                                  >  1:541427/1‑149 (MQ=255)                               accTCATGCAATATAAACATCTAGAAATAAAGATAACAATAGAATCTTAAGCCAACAAATAAGCTGAAAAAGTTTGTCTGCGATGCTCTCCTCTTTGACTCAAATTGGCCCCAAATGTTCCATCTTTTGGGGGAAAACTGTGCAGTGtt                                                                                                                 <  1:545080/149‑1 (MQ=255)                                     tGCAATATAAACATCTATAAATAAAGATAACAATACAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATATTTCATCTTTTGCGGGAAAACTATGCAATGTTGCCAgc                                                                                                           >  2:286946/1‑148 (MQ=255)                                               aCATCTATAAATAAAGATAACAATAGAAGATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGtt                                                                                                 <  2:345391/149‑1 (MQ=255)                                                          taaaGACAACAATAGAATATCAAGCCAACAACTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacaaa                                                                                      <  1:372177/149‑1 (MQ=255)                                                              gATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt                                                                                  <  1:218263/149‑1 (MQ=255)                                                                         aaTATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCATCTGTGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACt                                                                       >  2:590003/1‑149 (MQ=255)                                                                            atTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt                                                                                    <  2:149689/133‑1 (MQ=255)                                                                            atTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt                                                                                    >  1:149689/1‑133 (MQ=255)                                                                             ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCCTCATTTGTGGGAAAACTGTGCAATGTTGGCAGTCAGACTCTGTTACATAACAAAGGTTAAAGAAGCACTGccc                                                                   >  2:380412/1‑149 (MQ=255)                                                                                    aacaaATAAACTGAAAAAGTTTGTCTGCGATGCTTTCATCTATGAGGCAAAATGGACCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAGTCGTTTAAAAAAAAAAGTGTACAGAAAGACTGCGCATGTcaa                                                            >  2:592945/1‑147 (MQ=255)                                                                                     acaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGAt                                                           <  1:90388/149‑1 (MQ=255)                                                                                        aaTAAACTGAAGGAGTTTGTTCGCGATGCTTTCCTCTATGAGTCAAAATGGCCGCAAATGGTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGCTTTa                                                        <  2:495760/149‑1 (MQ=255)                                                                                                 aaaaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAGATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtt                                               >  1:393907/1‑149 (MQ=255)                                                                                                         tggccGCGATGCCTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                                       <  2:255907/146‑1 (MQ=255)                                                                                                                  cgCTTTCCTCTATGAGTCAAAATTGCCCCAAATGTTTCATCTTTTGTGGGAAAACTGTGCAGTGTTGGCATTCAAACTCGTTTACAAAACAAAGTGGACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAagcag                              <  1:233131/148‑1 (MQ=255)                                                                                                                    cTTTCC‑CTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCAt                           <  1:192924/149‑1 (MQ=255)                                                                                                                     tttCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAACAt                           >  1:615010/1‑149 (MQ=255)                                                                                                                                  tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCACGAAAATTAAACct              >  2:160575/1‑149 (MQ=255)                                                                                                                                    aaaaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAActct            >  2:370299/1‑149 (MQ=255)                                                                                                                                             ccAATTGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAATGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgt   >  2:7075/1‑149 (MQ=255)                                                                                                                                              cAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgtt  >  1:190943/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                  GCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTT  >  NC_000913_3_pae_tpiA/4542768‑4543057

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.