New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 2499276	12 (0.960)	4 (0.340)	4/244	1.1	24.8%	coding (606/1698 nt)	ypdA	sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
	?	NC_000913_3_pae_tpiA	= 2499293	13 (1.110)					coding (623/1698 nt)	ypdA	sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system

CCGCGTTGGGGATCGATATCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAGGCCAGCGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/2499158‑2499276 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagcgccAGCTTGGCCTGCCGCGCGGCGCTGGCCTCTTTTTCGCCCTCAACGCTTTGCACCAGAAGCACAATAAA  <  NC_000913_3_pae_tpiA/2499293‑2499226                                                                                                                                                                                             CCGCGTTGGGGATCGATATCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAG‑‑‑‑‑‑GCCAGCTTGGCCTGCCGCGCGGCGCTGGCCTCTTTTTCGC                                 <  2:49682/150‑1                                      TCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAGGCCAGCGCCAGCTTGGCCTGCCGCGCGGCGCTGGCCTCTTTTTCGCCCTCAACGCTTTGCACCAGAAGCACAATAAA  <  3:60413/150‑1                                                                                              TTGAGGGCGAAAAAGAGGCCAGCGCCAGCTTGGCCTGCCGCGCG                                                    <  1:19113/44‑1                                                                                              TTGAGGGCGAAAAAGAGGCCAGCGCCAGCTTGGCCTGCCGCGCG                                                    >  2:19113/1‑44                                                                                                                                                                                             CCGCGTTGGGGATCGATATCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAGGCCAGCGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/2499158‑2499276 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagcgccAGCTTGGCCTGCCGCGCGGCGCTGGCCTCTTTTTCGCCCTCAACGCTTTGCACCAGAAGCACAATAAA  <  NC_000913_3_pae_tpiA/2499293‑2499226

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.