Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,608	IS1 (+) +9 bp	7.6%	coding (572‑580/597 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)	13 (0.080)	11/176	NT	7.7%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542616	140 (0.950)					coding (580/597 nt)	fimE	regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	10 (0.060)	9/176	NT	6.0%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542608 =	140 (0.950)					coding (572/597 nt)	fimE	regulator for fimA

CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584133‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCA  >  NC_000913/4542608‑4542699                                                                                                                                                             CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTAT                                                          >  2:1579301/1‑99       AAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAA                                                    <  2:4494/99‑1          GTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAA                                                 >  2:1343113/1‑99                           GAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATA                                <  2:3048504/99‑1                           GAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATA                                <  2:3953353/99‑1                              CATAAAACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAAT                             <  2:4213360/99‑1                                   AACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAG                        >  1:4024525/1‑99                                    ACACTATCAATAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGA                       <  2:1728972/99‑1                                              TAAGTTGGAGTCATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGC             >  1:4113212/1‑99                                                         CATTACCAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCA  <  2:1949861/99‑1                                                                                                                                                             CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584133‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCA  >  NC_000913/4542608‑4542699

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ 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.