New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4542598 =	25 (0.540)	6 (0.140)	6/264	5.1	16.6%	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 =	37 (0.850)					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.

TCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTT  >  NC_000913_3_pae_tpiA/4542771‑4543060                                                                                                                                              |                                                                                                                                                     tCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTCTAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCa                                                                                                                                               >  1:28464/1‑149 (MQ=255)      cTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCttt                                                                                                                                          >  2:50482/1‑149 (MQ=255)       tCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAAGAAAGATAACAATAGGATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCTTCTATGAGTCAAAATGGCCCCAAATGTTTCATCtttt                                                                                                                                         >  1:720586/1‑149 (MQ=255)        cATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGtt                                                                                                                                                  <  2:111935/139‑1 (MQ=255)        cATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGtt                                                                                                                                                  >  1:111935/1‑139 (MQ=255)                    cAAAAACCACCTCATGCAATATAAAACTCTTTAATTAAGTATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgt                                                                                                                            >  1:198318/1‑149 (MQ=255)                          ccaccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                                                                                                      <  1:747420/149‑1 (MQ=255)                             ccTAATGAAAAATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAAAAAAAAAAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTg                                                                                                                   <  2:530141/149‑1 (MQ=255)                                cATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCa                                                                                                                <  1:50482/149‑1 (MQ=255)                                 aTGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCa                                                                                                                <  1:137405/148‑1 (MQ=255)                                 aTGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCa                                                                                                                >  2:137405/1‑148 (MQ=255)                                 aTGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAg                                                                                                               >  2:660170/1‑149 (MQ=255)                                   gCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAAAAAATAAACTGAAAAAGTTTGTCAGCGATGCTTTCCTCTATGAGTCAAAATGGCTCCAACTGTTTCATCTTTTGGGGGAAAACTGTGCAGAGTTGGCAGTc                                                                                                             >  1:239244/1‑149 (MQ=255)                                      atatAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCaaa                                                                                                          <  2:274202/149‑1 (MQ=255)                                         taAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTc                                                                                                       >  2:63898/1‑149 (MQ=255)                                            aCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGtt                                                                                                    <  1:660170/149‑1 (MQ=255)                                              aTCTATAAATAAAGATAAAAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCGTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGGTTa                                                                                                  >  1:201737/1‑149 (MQ=255)                                               tCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACGCGTTTac                                                                                                 <  2:67984/149‑1 (MQ=255)                                                  ataaataaAGATAACAATAGAATATTAAGCCAACAAATAAAATGAAAAAGTTTGTCCGCGATGCTTTCCTCTATAAGTCAAAATGGCCCCAAATGTTTCATCTTTTGTGGGAAAACTGTGCCGTGTTGGCAGCCAAACTCGTTTacaaa                                                                                              >  2:454874/1‑149 (MQ=255)                                                        aaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAg                                                                                        <  2:479043/149‑1 (MQ=255)                                                         aaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCAAAAAAGCGTGGTCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAACCTCGTTTACAAAACAAAgt                                                                                       >  1:396488/1‑149 (MQ=255)                                                         aaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATAGGACCAGATGTTTCAGATTTTGGGGGGAAACTGTGCAGTGTTGTGAGTCAAACGCGTTTACAAAACAAAgt                                                                                       >  1:187650/1‑149 (MQ=255)                                                          aGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAACCTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtg                                                                                      >  2:193759/1‑149 (MQ=255)                                                            aTAACAATAGAATATTACGCCAACGAATAAACTGAAACAGTTTGTCCGCGATTCTTTCCTCTATGAGTCACAATGGCCCCAAATGTTTCATCTCTTGGGGGAAAACTGTGCAGTGTTGGCAGTCATACTCTTTTACAAAACAAAGTGTa                                                                                    <  1:753898/149‑1 (MQ=255)                                                                        tatTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGc                                                                        <  1:53692/149‑1 (MQ=255)                                                                                caacaaATCAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTGTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAATCGTTTCCAAAACAAAGTGTACAGCACGACTGCCCATGTCg                                                                >  2:363290/1‑149 (MQ=255)                                                                                    aaaTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGAttt                                                            <  1:63898/149‑1 (MQ=255)                                                                                     aaTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTa                                                           >  1:785809/1‑149 (MQ=255)                                                                                            tGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCACGTCGATTTAGAAATAg                                                    >  2:201791/1‑149 (MQ=255)                                                                                              aaaaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCACCTGTGTTTGGGGGGTGTGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtt                                                  <  2:785809/149‑1 (MQ=255)                                                                                                 aaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGttttt                                               >  1:209261/1‑149 (MQ=255)                                                                                                 aaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATGTAGAAATAGttttt                                               >  1:297470/1‑149 (MQ=255)                                                                                                      tGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                                          <  2:209261/149‑1 (MQ=255)                                                                                                                               tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAAct                 >  1:255399/1‑149 (MQ=255)                                                                                                                               tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTCGCAAGCAAAGTAGCATGAAAATTAAAAct                 >  1:354682/1‑149 (MQ=255)                                                                                                                                  aaaTGGCCCCAAATGTTTCAACTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTg              <  2:32376/149‑1 (MQ=255)                                                                                                                                   aaTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTgg             <  2:198318/149‑1 (MQ=255)                                                                                                                                            aaaTGTTTCATCTTTTGGGGGAAAACTGTGCAGTACTCACAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAAGCgttg    >  2:176589/1‑149 (MQ=255)                                                                                                                                              aTGTTTCATCTTTTAGGGGAAAACTGTGCAGTTTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgttgtt  <  1:501449/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                     TCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTT  >  NC_000913_3_pae_tpiA/4542771‑4543060

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.