New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 848580	114 (0.940)	5 (0.050) +CTGAAAAAAAAAAA	3/252	8.9	3.6%	intergenic (+585/‑295)	trxB/USA300HOU_RS04145	Thioredoxin reductase/Nucleotide‑binding protein
	?	USA300TCH1516_ALE	2665075 =	182 (1.500)					intergenic (+310/+128)	pitA_2/USA300TCH1516_02535	L‑methionine sulfoximine/L‑methionine sulfone acetyltransferase/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTATGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/848470‑848580 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGT  >  USA300TCH1516_ALE/2665075‑2665131                                                                                                                ||||||||||||||                                                          aAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCGCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTGTTACAAG                                          <  2:670250/140‑1         ATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCC‑CGCCCCAACTCGCATTGCCTGTAGAATTCCTTTTTGAAATCCTCTGTGTTGGGGCCCTTGAAAAAAAAAAAAAAAAGCTTATTACAAGCGCATTTT                                  <  2:1222989/141‑1                                 tcctctTCTGTGTTGGGACCCACGCCCCAACTCGCATTGCCTGTAAAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATA           <  2:513776/135‑1                                 tcaactTCTGTGGTGGGACCCACACCCCGACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACAAAAAAAAAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATA           <  2:918816/135‑1                                         ttTGTTGGGGCCC‑CGCCCCAACTCGCATTGCCTGTAGAATTCCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTATTACAAGCGCATTTTCGTTCAGTCAATTACTGCCAATATAACTTcgt  <  2:1039849/139‑4                                                                                                                ||||||||||||||                                                          CAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTATGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/848470‑848580 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGT  >  USA300TCH1516_ALE/2665075‑2665131

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.