New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	18 (0.120)	3 (0.020)	3/512	NT	5.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	82 (0.560)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

CCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGTTTATATTGCATGAGGTGGTTTTTGGAGAGAAGAATGAGGAAGATGCGTCGAGCCACAGAAACGTTAGCTTTACATATAGCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4542989‑4542682 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATCAAACCGTTCAGTTAGGACA  >  NC_000913/4542996‑4543290                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             CCATTTTGAGTCATAGAGGAAAGCATCGCGGACAAACTGTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGTTTATATTGCATGAGGTGGTTTTTGGAGAGAAGAATGAGGAAGATGCGTCGAGCCACAGAAACGTTAGCTTTACATATAGCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTT                                                                                                                                                                                                                                                                                                                 <  1:410944/300‑1                                                                                          TGTTTATATTGCATGAGGTGGTTTTTGGAGAGAAGAATGAGGAAGATGCGTCGAGCCACAGAAACGTTAGCTTTACATATAGCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCC                                                                                                                                                                                                                                                                                                           <  1:501639/217‑1                                                                                          TGTTTATATTGCATGAGGTGGTTTTTGGAGAGAAGAATGAGGAAGATGCGTCGAGCCACAGAAACGTTAGCTTTACATATAGCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCC                                                                                                                                                                                                                                                                                                           >  2:501647/1‑217                                                                                                                                                                           GCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTC                                                                                                                                                                  >  1:1427389/1‑273                                                                                                                                                                           GCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTC                                                                                                                                                                  <  2:1427430/273‑1                                                                                                                                                                                                                                                          ATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCC                                                                                                                                                                                                                                                                                                            >  1:736868/1‑56                                                                                                                                                                                                                                                          ATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCC                                                                                                                                                                                                                                                                                                            <  2:736877/56‑1                                                                                                                                                                                                                                                                                                    GGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACCAAGTGTACCGAACGACTGCCCATGTCGATTGAGAAATAGTTTTTTTAAAGGAAAGCAGCATGAAAATTCAAACTCTGGCCATCGTTGTTCTTTCGGCTCTGTCCCTAAGTTCTACAGCGGCTCTGGCCGCTGCCCCGCCGGTTAATAGTGGCACCGTTCACTTTCAAGGTGAAGTTGTTACATCCGCTTTCTCAGTTAATGCCGGCTCTTTTGCGCCAACCGTT             >  2:888701/1‑301                                                                                                                                                                                                                                                                                                              GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTCATGGTGGGACCGTTCACTTTAAAGG                                                                    >  1:89783/1‑236                                                                                                                                                                                                                                                                                                              GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATTGTGGGACCGTTCAC                                                                            >  1:1004616/1‑228                                                                                                                                                                                                                                                                                                              GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGG                                                                    <  2:89787/236‑1                                                                                                                                                                                                                                                                                                              GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCAC                                                                            <  2:1004644/228‑1                                                                                                                                                                                                                                                                                                               aCCCAAATTGTTCATATTTTGGGGGAAAACTGTGAAGTGGTGGCCGTCAAACTAGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACGCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTGCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATCAAACCGTTCAGTTAGGAC   <  1:912421/299‑1                                                                                                                                                                                                                                                                                                               CCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTCCAGAACGACTGCCCATGTCGCTTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGACAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGCCCGTTCACTGTAAAGGGGAAGTTGTTAACGCAGCTTGCGCCGTTGATGCAGGCTCTGTTGATCACACCGTTCAGTTCGGCCA  >  2:159620/1‑301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             CCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTCTATTGTTATCTTTATTTATAGATGTTTATATTGCATGAGGTGGTTTTTGGAGAGAAGAATGAGGAAGATGCGTCGAGCCACAGAAACGTTAGCTTTACATATAGCGGAGGTGATGTGAAATTAATTTACAATAGAAATAATTTACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4542989‑4542682 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATCAAACCGTTCAGTTAGGACA  >  NC_000913/4542996‑4543290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.