Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,073	IS1 (+) +9 bp	6.1%	coding (37‑45/597 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)	5 (0.050)	4/176	NT	5.5%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542081	77 (0.920)					coding (45/597 nt)	fimE	regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	5 (0.050)	5/176	NT	5.5%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542073 =	77 (0.920)					coding (37/597 nt)	fimE	regulator for fimA

AAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584100‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGTATT  >  NC_000913/4542073‑4542162                                                                                                                                                                                            AAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAG                                                                                         >  1:810794/1‑99                                                    CATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGT                                      >  1:971342/1‑99                                                              ACATAAAACACTATCAATAAGTTGGAGTCATTACCCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGT                            <  1:653682/99‑1                                                                   AAACACTATCAATAAGTTGGAGTCATTACCCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCA                       <  1:971966/99‑1                                                                              ATAAGTTGGAGTCATTACCCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGG            >  2:1888389/1‑99                                                                                        GTCATTACCCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGTATT  >  1:1992796/1‑99                                                                                                                                                                                            AAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584100‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGTATT  >  NC_000913/4542073‑4542162

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