Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	4,542,372	IS1 (–) +9 bp	coding (336‑344/597 nt)	fimE →	regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1979270	NA (NA)	42 (0.890)	39/484	0.3	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	4542372 =	0 (0.000)					coding (336/597 nt)	fimE	regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	53 (1.120)	49/482	0.1	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 4542380	0 (0.000)					coding (344/597 nt)	fimE	regulator for fimA

ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCC  >  NC_000913/1979163‑1979271                                                                                                            |  accaccCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCAccc  >  1:57628/1‑109 (MQ=11) accaccCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCAccc  <  2:57628/109‑1 (MQ=11)                                                                                                            |  ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCC  >  NC_000913/1979163‑1979271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.