New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4099447 =	287 (1.180)	3 (0.010)	3/274	NT	1.1%	coding (802/849 nt)	rhaR	transcriptional activator of rhaSR
	?	NC_000913	4099477 =	263 (1.090)					coding (832/849 nt)	rhaR	transcriptional activator of rhaSR
Rejected: Frequency below/above cutoff threshold.

ATTGAGATGACGCCACTGGCTGGGCGTCATCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4099479‑4099447 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAA  >  NC_000913/4099477‑4099625                                                                                                                                                                                        ATTGAGATGACGCCACTGGCTGGGCGTCATCTCAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCT                                  >  1:2125175/1‑150    GAGATGACGCCACTGGCTGGGCGTCATCCCAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGA                                                                                                   >  1:340866/1‑82    GAGATGACGCCACTGGCTGGGCGTCATCCCAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGA                                                                                                   <  2:340866/82‑1                                 CAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAA  <  1:3579081/150‑1                                 CAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAA  <  1:3579139/150‑1                                 CAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAA  <  2:164143/150‑1                                                                                                                                                                                        ATTGAGATGACGCCACTGGCTGGGCGTCATCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4099479‑4099447 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cAATTCGCAGAAAGATTAATTCGCCATGCCGATGCCGACGATGTTAGCGGCGACAATAATCACCACACAACCGAGGCTCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAA  >  NC_000913/4099477‑4099625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ 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.