New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3559450 =	10 (0.800)	4 (0.330)	4/248	1.1	34.0%	coding (1183/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913_3_pae_tpiA	3559496 =	6 (0.500)					coding (1229/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression

TACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/3559498‑3559450 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcgcgGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGT  >  NC_000913_3_pae_tpiA/3559496‑3559571                                                                                                                               TACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGA                   <  3:34409/108‑1 TACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGA                   >  4:34409/1‑108  ACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGT  <  1:42355/124‑1  ACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGT  >  2:42355/1‑124                                                                                                                               TACCGCGCCATGTTGCCTGGGGAGAGGTCGCAAAAGCCAACCAGGCGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/3559498‑3559450 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcgcgGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGT  >  NC_000913_3_pae_tpiA/3559496‑3559571

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.