New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	11 (0.430)	8 (0.330)	7/474	1.1	39.4%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	14 (0.570)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

GCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCA  >  NC_000913/4542461‑4542935                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                      gcgtttatgaATTGGCGGAGCGTGGTGCAGATTCTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCCCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATGGGGGCCAttttgactcatagaggaaag                                                                                                                                                                                                                                   <  2:220737‑M1/246‑21 (MQ=255)    aacggtcccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGtt                                                                                                                                                                                                                               >  2:245400‑M1/219‑251 (MQ=255)       ggtcccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAATTAAGTTACg                                                                                                                                                                                                                            <  1:143036‑M1/36‑1 (MQ=255)       aTGAATTGGCGGCGCGAGGTGCAGCTACTGGTTTAATTCAGGCTCATCTCGGGAATCGAACTATTCGCCATACTGTGCGTTATACAGCAAGTAATGCTGCTCGTTTAGCCGGATTATGGGTAAGCAATAAGCTCATAAACGAAAAATTAAAAAGAGAAGAGGGTTGATTTCACTTATTGATCATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGttccg                                                                                                                                                                                                                            >  2:115865/1‑248 (MQ=255)           aTTGGCGGAGCGGGGGGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGCGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggac                                                                                                                                                                                                                         >  1:177733‑M1/1‑220 (MQ=255)                    gtgtggtgcaGATACTCTGTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagatgaaagcatcgcggacaaactttttc                                                                                                                                                                                                               <  2:210422‑M1/249‑41 (MQ=255)                    gCGTGGTTCAGATACTTGTTTAAGCCAGGATTATGTCGGTCATCGAAATAGTCGCCATACTGGGCGGTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAATAGGTGTGATGTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAatttgactcatagagtaaagcacggcgaactaactttttc                                                                                                                                                                                                               <  2:86744‑M1/251‑41 (MQ=255)                       gggtgCAGAAACTCGTTTAAGTAAGTATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                                                                                                                            <  2:80433/250‑1 (MQ=255)                                                           gaaTCGAAATATTCGCCATACTGTGCTTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTg                                                                                                                                                                        <  1:159684/249‑1 (MQ=255)                                                                                tgtgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcat                                                                                                                                                   >  2:195694‑M1/1‑151 (MQ=255)                                                                                   gcgtgagaCCGCCATTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAATGTTAAAAAGATGAAAAAACGACAAAAAGCATTTAACTGTTTGATAGGTAAATTATTGCTAtt                                                                                                                                                <  2:245117/244‑1 (MQ=255)                                                                                          aacGCCATTAATGCTGCTCGTTTTGCAGGATTAAGGGAAAGAAATAATCTCATAAAAGAAAAATTAAAAAGAGAATAGGTTTGATTTAACTTATTGATAATAAAGGTAAAAAAACAAATAAATACACGACAATTGGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTATCTCAAGCATTAAAATATTAAAAAACGACAAAAAGCATCTATCAGTTTGATATGTAAATTATTTCTATTGTAaatt                                                                                                                                         <  2:84940/249‑1 (MQ=255)                                                                                                         gctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc                                                                                                                            <  2:221415/249‑1 (MQ=255)                                                                                                                  gCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTatat                                                                                                                 >  1:125739/1‑251 (MQ=255)                                                                                                                     aaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTa                                                                                                              >  1:28029‑M1/106‑251 (MQ=255)                                                                                                                         tATGGGAAAGAAATAATCTCATAAACGGAAAATTAAAAAGTGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTACCTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGc                                                                                                          >  2:90018/1‑251 (MQ=255)                                                                                                                          actatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacagTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCt                                                                                                         >  1:87106‑M1/101‑251 (MQ=255)                                                                                                                            tatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTa                                                                                                        <  1:180072‑M1/152‑1 (MQ=255)                                                                                                                                      taatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCtgtg                                                                                             >  2:218412/1‑251 (MQ=255)                                                                                                                                       cgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTgg                                                                                            <  2:177733‑M1/164‑1 (MQ=255)                                                                                                                                        atCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgta                                                                                             >  2:143036‑M1/1‑95 (MQ=255)                                                                                                                                                                                                aaGTTAAAAAACCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATACTAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAAcctc                                   >  2:228130/1‑248 (MQ=255)                                                                                                                                                                                                         aaaCAAATAAATACAAGACAATTGGGGCCActttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcaggaggtggtttttggatagaagaatgaggaagatgcgtcgagccacagaaacgttatctttacatatagcggaggtgatgtgaaattaagttacaatagaaagaatttacatatcatacagt                          <  2:134480‑M1/251‑222 (MQ=255)                                                                                                                                                                                                             aaataaatACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttttcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagataagaatgaggaagatgcgtcgagccacagaaacgttagctttacatatagcggaggttatgtgaaattaatttacaatagaaataatttacatatcaaacagttaga                      <  1:262783‑M1/251‑226 (MQ=255)                                                                                                                                                                                                                                 gggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGAGAACAATAGAATATTAAGCca  <  1:102094/251‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                      GCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCA  >  NC_000913/4542461‑4542935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ 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.