New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3741741 =	48 (0.990)	4 (0.090)	4/280	6.9	8.1%	coding (792/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
	?	NC_000913_3_pae_tpiA	3741759 =	45 (0.960)					coding (774/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGAAAAATCTCCTGAAACCACTGCGTGAAACCGCGCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/3741778‑3741741 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcagTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGC  >  NC_000913_3_pae_tpiA/3741759‑3741905                                                                                                                                                                                           AGAAAAATCTCCTGAAACCACTGCGTGAAACCGCGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAA                                                        <  1:665047/131‑1 AGAAAAATCTCCTGAAACCACTGCGTGAAACCGCGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAA                                                        >  2:665047/1‑131               AAACCACTGCGTGAAACCGCGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACA                                      >  1:584595/1‑135               AAACCACTGCGTGAAACCGCGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACA                                      <  2:584595/135‑1                                   gcgGTGGTTGCAGGAGATTTTTCCCGCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACCCGGCGTACGGCACCCGCCCATGAATATCAAACTCCGGAACAGCAAGACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATC    <  1:714923/146‑1                                     AGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGC  >  1:82325/1‑149                                                                                                                                                                                           AGAAAAATCTCCTGAAACCACTGCGTGAAACCGCGCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/3741778‑3741741 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcagTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGC  >  NC_000913_3_pae_tpiA/3741759‑3741905

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ 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.