New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	14 (0.480)	5 (0.180)	5/466	2.3	25.3%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	16 (0.570)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

CTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAA  >  NC_000913/4542767‑4543236                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                            cTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGaa                                                                                                                                                                                                                              >  1:278250/1‑250 (MQ=255)          atGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAATCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATATAATATTAAGCCAACAAATAAACCGAAATAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCa                                                                                                                                                                                                                     <  1:214581/250‑1 (MQ=255)                              aaaTTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatc                                                                                                                                                                                                  >  1:115239‑M2/1‑191 (MQ=255)                                    attTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtttttatttgtttttttaactttattatcaataagttaaatcaaacctt                                                                                                                                                                                           <  1:111453‑M2/251‑67 (MQ=255)                                           aTCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctt                                                                                                                                                                                    >  1:1944‑M2/1‑178 (MQ=255)                                           aTCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGATCGACGCATCTTCCTTATTCTTCTATCAAATCACCACCTCACGCACTATAAACATCCATATCTATAGCAAACACTATTATATTAAGCCAACAAATAAACTGAAAAACCTTGTCCGCAATGCGTTCATCTAT‑AAACTACATCGGCCCCAAATGTTTCAACTTTTCGGGAGAAACTGTACAGTGGTGCCCGTTAAACTCGTTTacaacactaagg                                                                                                                                                                                   >  1:222994/1‑243 (MQ=255)                                                                                                               aaaCCCCCTCATGCAATATAACCATCTCTACATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGTGGGAAAACTGTTCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAATGAAAGCAGCattaaaattaaa                                                                                                                >  1:89521/1‑250 (MQ=255)                                                                                                                aacccccacATGCAATAAAAACAGCTATAAATAAAGATAACAATAGAATATTAATCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCGTTCCTGTATGAGTCAAAAT‑GGCCTCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAAc                                                                                                              <  2:270057/243‑1 (MQ=255)                                                                                                                         aTGCAATAAAAAAAACTATAAAAAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCTGCTATGCTTTCCTCTATGAGGCAAAAT‑GGTCCCAAATATTTCATCTTTTGAGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTATAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACGCTGGCAAt                                                                                                     <  2:278250/251‑1 (MQ=255)                                                                                                                             aaTATAAACAGCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTTAAAAAGGTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgtt                                                                                                 <  1:137602/251‑1 (MQ=255)                                                                                                                                  aaaCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCt                                                                                            >  1:274909/1‑251 (MQ=255)                                                                                                                                           taaataaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacaggctggcgaatatttct                                                                                     <  1:14036‑M2/250‑169 (MQ=255)                                                                                                                                                            ataaTATTCAGCCAGAAAATAAACTGAAAAACGTTGTCCGCGAGGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTATCATCTTTTGTGGGAAAACTGTGTAGTGTTGACAGTAACACTCGTTTCCAAAACAAAGTGTACAGATAGACTGACAATGTCGATTTAGAAATAGTTTTTGGAAAGGAAAGCACCATGAAAGTTAACACTATGGCAATCGTTGTTCTGTCGGCCATGTCCGTCAgataaaccg                                                                  >  2:182888/3‑243 (MQ=255)                                                                                                                                                                     aGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTgg                                                         >  1:4647/1‑251 (MQ=255)                                                                                                                                                                          acaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAGTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTTTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCt                                                    >  1:155870/1‑251 (MQ=255)                                                                                                                                                                                     gAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattattgctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgcaccacg                                           >  2:59927‑M2/1‑40 (MQ=255)                                                                                                                                                                                                             ccgctaagAGTCAAAAT‑GGCCCCAAATGGTGCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCAGGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGCTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTaa                 <  1:256469/244‑1 (MQ=255)                                                                                                                                                                                                                        cAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCTCTTTAAAgggggtgttg      >  2:10962/1‑245 (MQ=255)                                                                                                                                                                                                                           aaT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGtt                         <  1:279525/229‑1 (MQ=255)                                                                                                                                                                                                                           aaT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGtt                         >  2:279525/1‑229 (MQ=255)                                                                                                                                                                                                                            aT‑GGCCCCAAATGTTTCAACTTTTGGGGGAAAACTGTGCAGTGGTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTaa  <  1:41627/251‑1 (MQ=255)                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                            CTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAT‑GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAA  >  NC_000913/4542767‑4543236

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.