New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 456294	44 (0.770)	3 (0.050)	3/262	6.0	7.1%	intergenic (+216/‑150)	speC_5/tst_4	Exotoxin type C/Toxic shock syndrome toxin‑1
	?	USA300TCH1516_ALE	= 456337	35 (0.630)					intergenic (+259/‑107)	speC_5/tst_4	Exotoxin type C/Toxic shock syndrome toxin‑1
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGTGTTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/456159‑456294 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attTAAATATACTTGAATTATTCTTAATGAAAAACAAATATATTTTAATGTTCAGGTTAAA  <  USA300TCH1516_ALE/456337‑456280                                                                                                                                                                                                    TGTGGTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGAGAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACAT                                                             <  2:493969/135‑1                                       ATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTG‑‑TTATTCTTAATGAAAAACAAATATA                     <  2:549288/135‑1                                                                       TTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTTAAATATACTTGAATTATTCTTAATGAAAAACAAATATATTTTAATGTTCAGGTTAAA  >  1:3085/1‑124                                                                       TTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTTAAATATACTTGAATTATTCTTAATGAAAAACAAATATATTTTAATGTTCAGGTTAAA  <  2:3085/124‑1                                                                                                                                                                                                    TGTGTTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/456159‑456294 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attTAAATATACTTGAATTATTCTTAATGAAAAACAAATATATTTTAATGTTCAGGTTAAA  <  USA300TCH1516_ALE/456337‑456280

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.