Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,015	IS1 (+) +9 bp	13.9%	intergenic (+456/‑14)	fimB → / → fimE	regulator for fimA/regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583428 =	NA (NA)	15 (0.160)	13/174	NT	14.9%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542023	77 (0.930)					intergenic (+464/‑14)	fimB/fimE	regulator for fimA/regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	10 (0.110)	10/176	NT	10.3%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542015 =	78 (0.930)					intergenic (+456/‑22)	fimB/fimE	regulator for fimA/regulator for fimA

TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584107‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGG  >  NC_000913/4542015‑4542110                                                                                                                                                                                           TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGG                                                                                        >  1:766865/1‑99      TTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTAC                                                                                   >  1:349295/1‑99                                             CATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGA                                            >  2:1942980/1‑99                                               TTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAG                                          <  1:655060/99‑1                                                 ATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTT                                        >  1:1999630/1‑99                                                               CACTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCA                          >  1:1969579/1‑99                                                                 CTATCAATAAGTTGGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGG                        <  2:152006/99‑1                                                                              GGAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGG           <  1:2043445/99‑1                                                                               GAGTCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGG          >  2:1935745/1‑99                                                                                  TCATTACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCA       >  2:994018/1‑99                                                                                       ACCCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGG  >  2:87181/1‑99                                                                                                                                                                                           TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584107‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGG  >  NC_000913/4542015‑4542110

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.