New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	11 (0.510)	7 (0.330)	7/472	1.2	40.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	10 (0.480)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

GACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATA  >  NC_000913/4542432‑4542906                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                 gacgcATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAt                                                                                                                                                                                                                                  <  1:204229/247‑1 (MQ=255)                     ggCATGCTTGCGGTTATGAATTGGCGGAGCGGGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATc                                                                                                                                                                                                             <  1:43940/251‑1 (MQ=255)                             tGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCataaata                                                                                                                                                                                                      <  1:88021/250‑1 (MQ=255)                                       cccaccattaaccgtcgtggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAt                                                                                                                                                                                            >  2:49034‑M1/213‑251 (MQ=255)                                                         ggcagcggccagagccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaa                                                                                                                                                                           >  2:133248‑M1/195‑250 (MQ=255)                                                                      gccgctgtagaactgagggacagagccgacagaacaacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACg                                                                                                                                                             >  2:37622‑M1/182‑251 (MQ=255)                                                                              aTTATCTCGGGAATCAAAATTTTCGCCATGATGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGTTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGc                                                                                                                                                    <  2:142802/251‑1 (MQ=255)                                                                                                  atTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATGTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTa                                                                                                                                <  1:32621/251‑1 (MQ=255)                                                                                                    tcgaaatacttcgcgttaatccgacAGTAATGCTGCTCGGTTCGCCGGATTAAGGGAAATAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACGAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTTCGTATTTTTTCTCAAGCAGAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTaa                                                                                                                               <  1:199994/226‑1 (MQ=255)                                                                                                        cATACTTTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGTTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                                                                                                                                                                <  1:138291/181‑1 (MQ=255)                                                                                                        cATACTGTGCGTTATACCCCCCGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTAc                                                                                                                                                                                                >  2:138291/1‑181 (MQ=255)                                                                                                                                   gctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAA‑TGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaaga                                                                                                >  2:92967‑M1/1‑128 (MQ=255)                                                                                                                                         cGTTTTGACGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTcc                                                                                           <  2:23690/249‑1 (MQ=255)                                                                                                                                                                         tgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCg                                                           <  1:114192‑M1/168‑1 (MQ=255)                                                                                                                                                                         cATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAA‑TGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgttagctt                                                           <  1:92967‑M1/249‑160 (MQ=255)                                                                                                                                                                                  gttctgtacactttgttttgtaaacgagtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTc                                                 <  1:176397‑M1/178‑1 (MQ=255)                                                                                                                                                                                                         gATTTAACGTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAG‑GGGGCCAAACTGTCCATATCAGAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCTCTATATGTAAAGCTAACGTTTCTGCGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAaacac                         <  2:70530/251‑1 (MQ=255)                                                                                                                                                                                                             gtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAacca                          >  2:12608‑M1/47‑247 (MQ=255)                                                                                                                                                                                                             gtttgactgccaacactccacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAacca                          <  1:12608‑M1/201‑1 (MQ=255)                                                                                                                                                                                                                   aTTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAat               >  1:121326/1‑251 (MQ=255)                                                                                                                                                                                                                                 tAAAAAAACAAATAAATACAAGACAA‑TGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatgtatagatgtttatattgcatgaggtggtttttggagagaagaatgagtaagaggggtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaa  <  2:41353‑M1/250‑217 (MQ=255)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                 GACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATA  >  NC_000913/4542432‑4542906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ 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.