New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	17 (0.380)	3 (0.070)	3/464	2.5	14.9%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	18 (0.420)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Rejected: Frequency below/above cutoff threshold.

AACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGT  >  NC_000913/4542748‑4543230                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                     aaCGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTT‑GTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGt                                                                                                                                                                                                                                         >  2:163689/1‑251 (MQ=255)                                       tttCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGAAGCATATTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAATTGTTTCATTTTTTGGGGGAAAACTGTGCAGTGTTGGCAGt                                                                                                                                                                                                    >  1:17896/1‑251 (MQ=255)                                                   attaattTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTa                                                                                                                                                                                        <  2:219338/251‑1 (MQ=255)                                                                          atatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGAc                                                                                                                                                                 >  1:54822/1‑251 (MQ=255)                                                                          atatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCGCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGGCCGCGATGCTTTCCTCTATGAGTTAAAATTTCCCCAAATGTTTCATCTTTTGGGGGAAAACGGTGCAGTGCGGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACg                                                                                                                                                                   <  2:277087/249‑1 (MQ=255)                                                                                aaaGCTAACGTTTCTGTGGCTCGACGCATCCTCCTCCTTCTTCTCTCACAAAACCACCTCATCCAATATAAACATATATAAATACAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTATTCGCGATGCTTTCCACTATGAGTCAAAATGGCACCAAATGTTTCATCTTTTGAGGGAAAACTTTGCAGTGTTGGCAGTCAACATCTTTTACAAAACAAAGGGTACCGAACGACTGcccc                                                                                                                                                           >  2:300595/1‑250 (MQ=255)                                                                                                     cGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAATATAACAATAGACTATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCTATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACTAAGTGTACAGAACGACTGACCATGTCGATTTAGAAATAGtttt                                                                                                                                      <  2:118844/251‑1 (MQ=255)                                                                                                     cGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccata                                                                                                                                        >  1:112469‑M2/1‑139 (MQ=255)                                                                                                     cGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtt                                                                                                                                        <  2:256923/249‑1 (MQ=255)                                                                                                               tCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGGTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgttttgttaactttattatcaataagttaaatcaaacctctgcgctttttaatttttcggttatgagattattgctttcccataatccggcaaa                                                                                                                              >  2:184279‑M2/1‑129 (MQ=255)                                                                                                                   cATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGTCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACTACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAagca                                                                                                                        <  2:395605/251‑1 (MQ=255)                                                                                                                                                  tataAACATCTATAAATAAAGATAACAATAGAATATTAAGCAAACCAATAACCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccacaattgtcttgtctttatttgtttttttacctttattatcaataagttaaatcaaacctcttctctttttactttttcgtttatgagattatttctttcccctaatccggcaaaacgagcagcattactggaggtataacgcacagatagg                                                                                         <  1:27291‑M2/251‑158 (MQ=255)                                                                                                                                                                         aaCAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTc                                                                                                                                                       <  1:426859/166‑1 (MQ=255)                                                                                                                                                                         aaCAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTc                                                                                                                                                       >  2:426859/1‑166 (MQ=255)                                                                                                                                                                               aGAATATTAAGCCATCAAATAAACTGAAAAAATTTGTCCGCGATGCTTTCCTCTATGAGTGAAAATGGCCCCAAATGGTTCATCTTCTGGGGGAAAACGGTGCAGTGTTGGCAGTCAGTCGCTTGTACAAAACAAAGTGTATAGAACGACTGCCCAGGTCTATTTATAAGGAGTTTTTTGAAAGGAAAGCAGCATGAAAATTTAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAg                                                            <  1:212155/251‑1 (MQ=255)                                                                                                                                                                               aGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCACTCAGtactac                                                              >  2:179364/1‑249 (MQ=255)                                                                                                                                                                                                  tAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCATTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCac                                         >  1:13047/1‑251 (MQ=255)                                                                                                                                                                                                                        gATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGtt                   >  2:407855/1‑251 (MQ=255)                                                                                                                                                                                                                           gCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCAc                >  2:5598/1‑251 (MQ=255)                                                                                                                                                                                                                                        aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAg   <  1:220588/251‑1 (MQ=255)                                                                                                                                                                                                                                         gtaaacaTGGCCCCAAATGGTTCATCTTTTGGGGTCACCCTGTGCAGTGTTGCCAGTCAACCTCGTTTACAAAACAAAGTGTACAGAACCACCGCCCAGGTAGATTTAGAAATAGTTTCTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTATGGCCGTTGCCACGTCGGTTAATGGTGAGACCGTTCAAtttcagagggaagg  >  2:249515/7‑240 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                     AACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGT  >  NC_000913/4542748‑4543230

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.