Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,065	IS1 (+) +8 bp	8.2%	coding (29‑36/597 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)	12 (0.090)	12/176	NT	8.5%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542072	117 (0.920)					coding (36/597 nt)	fimE	regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	9 (0.060)	9/176	NT	6.5%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542065 =	117 (0.920)					coding (29/597 nt)	fimE	regulator for fimA

GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584129‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCG  >  NC_000913/4542065‑4542158                                                                                                                                                                   GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGT                                                                >  2:3616496/1‑99                  TCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGC                                               <  2:505412/99‑1                     GGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAG                                            >  1:406028/1‑99                      GCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGA                                           >  1:3009483/1‑99                         TTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGAT                                        <  2:2806294/99‑1                              TGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTG                                   <  1:2588971/99‑1                                    TAAAACACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTAT                             >  1:405079/1‑99                                         CACTATCAATAAGTTGGAGTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGT                        >  1:379159/1‑99                                                           GTCATTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGA      >  1:3394813/1‑99                                                               TTACCAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCG  >  1:2902731/1‑99                                                                                                                                                                   GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3584129‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCG  >  NC_000913/4542065‑4542158

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.