Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	4,542,428	IS1 (–) +9 bp	10.6%	coding (392‑400/597 nt)	fimE →	regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1978503 =	NA (NA)	9 (0.100)	9/176	NT	9.6%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 4542436	76 (0.910)					coding (400/597 nt)	fimE	regulator for fimA
*	?	NC_000913	3583428 =	NA (NA)	9 (0.100)	9/176	NT	9.6%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	4542428 =	76 (0.910)					coding (392/597 nt)	fimE	regulator for fimA

GCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583520‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAT  >  NC_000913/4542428‑4542510                                                                                                                                                                                  GCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGgcta                                                                               <  2:2082664/99‑5           AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCA                                                                     >  1:1351927/1‑99                               GAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCG                                                 >  1:2427723/1‑99                                     ACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATG                                           <  1:1782822/99‑1                                                   AAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGT                             >  1:2326635/1‑99                                                     AACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGG                           >  2:501600/1‑99                                                               TACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACT                 >  1:1323670/1‑99                                                               TACACTAAATCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACT                 <  2:346485/99‑1                                                                        TCAGTAAGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATT        >  2:1750857/1‑99                                                                              AGTTGGCAGCATCACCCGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAT  <  2:1485820/99‑1                                                                                                                                                                                  GCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583520‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAT  >  NC_000913/4542428‑4542510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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.