Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,511	IS1 (+) +9 bp	5.9%	coding (475‑483/597 nt)	fimE →	regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583428 =	NA (NA)	4 (0.050)	4/176	NT	4.7%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542519	72 (0.900)					coding (483/597 nt)	fimE	regulator for fimA
Rejected: Frequency below/above cutoff threshold.
*	?	NC_000913	= 3584195	NA (NA)	5 (0.060)	5/176	NT	5.9%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542511 =	72 (0.900)					coding (475/597 nt)	fimE	regulator for fimA

AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584118‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAAT  >  NC_000913/4542511‑4542597                                                                                                                                                                       AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTATCTCGGGCATCGAAATATT                                                                    >  2:1261448/1‑99 AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTATCTCGGGCATCGAAATATT                                                                    <  2:469687/99‑1                                      ATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTC                               >  1:362319/1‑99                                                   ACACTATCAATAAGTTGGAGTCATTACCTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATT                  >  2:1824258/1‑99                                                                   GGAGTCATTACCTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAAT  <  2:1403745/99‑1                                                                                                                                                                       AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584118‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAAT  >  NC_000913/4542511‑4542597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.