New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	11 (0.630)	3 (0.180)	3/274	1.6	18.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	16 (0.970)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Rejected: Frequency below/above cutoff threshold.

CGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATC  >  NC_000913/4542476‑4542902                                                                                                                                                                                                                |                                                                                                                                                                                                                             tggAGCGTGGTGCAGATACTCGTTTAATTCAGGATTAACTCGGGCATCCAAATAATCGCCATACTGTGCGATATACCGCCAGTAATGCTGCTCGTTTTGCCGGAATATGGGAAAAAAATAATCTCATAAACGCAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGCAAATTGGGACCAAACTAACCATATCCTAAATAAGTTACGTAttttttt                                                                                                                                                                                  >  1:64413/2‑250 (MQ=255)                                                         ngCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttt                                                                                                                                                                                     >  1:85696/2‑192 (MQ=255)                                                          nccATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGT‑ACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                                                                                          >  1:282623/2‑217 (MQ=255)                                                           ncATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAACAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaaa                                                                                                                                                                      >  1:358076/2‑205 (MQ=255)                                                                      gTTAAACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTggggn                                                                                                                                                                                                                        <  1:88607/144‑2 (MQ=255)                                                                                           ctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTACCTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTc                                                                                        >  1:149560/1‑251 (MQ=255)                                                                                              gTTTTGCGGGATTATGGGAAAGAAATAATCTCAAAAACAAAAAATTAAAAAGAGAAGAGGTTTGATT‑AACTTTATTGATAATAAAGTAAAAAAAACAAATAAATACAAGACAATTGGGGcc                                                                                                                                                                                                                       <  1:156992/121‑1 (MQ=255)                                                                                                                                   cGNNNNNTTANAAAGAGAAGAGGTTTGATTTAACTA‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGT‑ACGTATTTTTTCTAAAGCATAAAAATATTAAAAAAc                                                                                                                                                          <  2:282623/144‑1 (MQ=255)                                                                                                                                              acactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttct                                     <  1:142670‑M1/185‑1 (MQ=255)                                                                                                                                                                                      tAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGAAAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAcc                                                                                          >  1:244519/1‑159 (MQ=255)                                                                                                                                                                                       aaaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCATCAATAAGTTACGCATTTTTTCTCAAGCATAAAAATATTCAACAACGACAAAAAGCATCTACCTGtt                                                                                                                                     >  1:182372/1‑115 (MQ=255)                                                                                                                                                                                        gttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAg                                                                                                                                                                                                <  1:413551‑M1/31‑1 (MQ=255)                                                                                                                                                                                               cccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGAATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAatataaaaatc  <  1:382521‑M1/221‑5 (MQ=255)                                                                                                                                                                                                            ccAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAGTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCGCCGCTATATGTAAAGCTAACGGTTCTGTGGCTCGACGCATCTTCCTCATGCTTCTCTCCAAAAGCCACCTCATGCAAGATAAACATc  <  1:118546/224‑1 (MQ=255)                                                                                                                                                                                                                |                                                                                                                                                                                                                             CGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTT‑ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATC  >  NC_000913/4542476‑4542902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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.