New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4542598 =	15 (0.410)	5 (0.150)	5/262	4.0	23.8%	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 =	18 (0.530)					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.

TCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGT  >  NC_000913_3_pae_tpiA/4542774‑4543059                                                                                                                                           |                                                                                                                                                    tCCTCATTCTTCTCTCCAAACACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATACGCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAATTGtcttgtat                                                                                                                                           <  1:219333/149‑8 (MQ=255)      aTTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCGACAAATGTTTCATCTTTTgg                                                                                                                                      >  1:209143/1‑149 (MQ=255)                  aaaaaCCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGACTATTAAGCCAACAAATACACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAACATGCCACCAAATACTTCATCTTTTGGGGGAAAACtgtg                                                                                                                          >  2:438792/1‑149 (MQ=255)                                                          tAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCtttt                                                                                                                                        <  1:570766/95‑1 (MQ=255)                                                          tAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCtttt                                                                                                                                        >  2:570766/1‑95 (MQ=255)                                                              aaTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAGATGGCCCCAAATGTTTCATCTTTTGGGGG‑AAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAAc                                                                             >  1:331289/1‑149 (MQ=255)                                                                  gAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGAc                                                                          >  1:19634/1‑149 (MQ=255)                                                                           gCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTCCAGAACGACTGCCCATGt                                                                 >  2:39334/1‑149 (MQ=255)                                                                                 aaaTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGCCAAAATGGCCCCAAATGTTTCATCTTTTGGAGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACTAAACAAAGTGTACGTGACGACTACCCATGTCGAtgt                                                           >  1:124323/1‑147 (MQ=255)                                                                                  aaTAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTa                                                          <  1:482301/149‑1 (MQ=255)                                                                                             aaaGTTTGCTGGCGATGTTTTCCTCTATGAGTCAAAATGGCCCCATATGTTTTATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttt                                               <  2:308871/149‑1 (MQ=255)                                                                                                       cgcgATGCTCTCCGTGATGAGTAAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGGCGATTTAGAAATAGTTTTTTgaaaggaa                                     <  2:54966/149‑1 (MQ=255)                                                                                                            tGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                                          <  2:369047/59‑1 (MQ=255)                                                                                                            tGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgtg                                                                                                                          >  1:369047/1‑59 (MQ=255)                                                                                                                    tctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGaaaa                        >  1:49829/1‑149 (MQ=255)                                                                                                                    tctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGaaaa                        <  2:365347/149‑1 (MQ=255)                                                                                                                     ctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaaggaaa                                    >  1:133868/1‑136 (MQ=255)                                                                                                                     ctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaaggaaa                                    <  2:133868/136‑1 (MQ=255)                                                                                                                                          aaTGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTTGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgttgt  <  1:516549/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                    TCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGT  >  NC_000913_3_pae_tpiA/4542774‑4543059

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.