New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	W3110S.gb	= 4547372	5 (0.270)	10 (0.660)	7/82	NT	62.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin
	?	W3110S.gb	= 4547668	8 (0.520)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin

GGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  W3110S.gb/4547309‑4547372 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTC  <  W3110S.gb/4547668‑4547605                                                                                                                                  GGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATT                                                                         >  1:1298332/1‑57        TTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAG                                                     <  1:660412/70‑1        TTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATA                                                      <  1:1485865/69‑1         TTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAG                                                   >  1:1727917/1‑71         TTAACCTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTT                                                              <  1:1103167/60‑1                ATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAG                                              <  1:1361732/69‑1                                    AACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAG                                              <  1:26064/49‑1                                    AACAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAG                                              <  1:806297/49‑1                                      CAAATAAATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTT                      <  1:203695/71‑1                                             ATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAAC                                <  1:156501/54‑1                                             ATACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAAC                                <  1:739579/54‑1                                               ACAAGACAATTGGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTT                              >  1:1379575/1‑54                                                          GGGGCCATTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTC  >  1:491908/1‑71                                                                                                                                  GGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  W3110S.gb/4547309‑4547372 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggggccaTTTTGACTCATAGAGGAAAGCATCGCGGACAAACTTTTTCAGTTTATTTGTTGGCTTAATATTC  <  W3110S.gb/4547668‑4547605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.