New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 848580	114 (0.940)	6 (0.050) +CTGAAAAAAAAAA	5/254	7.8	5.2%	intergenic (+585/‑295)	trxB/USA300HOU_RS04145	Thioredoxin reductase/Nucleotide‑binding protein
	?	USA300TCH1516_ALE	2866847 =	127 (1.050)					intergenic (‑246/+207)	USA300HOU_RS14695/noc_2	hypothetical protein/Nucleoid occlusion protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTATGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/848470‑848580 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAT  >  USA300TCH1516_ALE/2866847‑2866922                                                                                                                |||||||||||||                                                                             aAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCGCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTGTTACAAG                                                            <  2:670250/140‑1         ATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCC‑CGCCCCAACTCGCATTGCCTGTAGAATTCCTTTTTGAAATCCTCTGTGTTGGGGCCCTTGAAAAAAAAAAAAAAAAGCTTATTACAAGCGCATTTT                                                    <  2:1222989/141‑1                                 tcctctTCTGTGTTGGGACCCACGCCCCAACTCGCATTGCCTGTAAAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATA                             <  2:513776/135‑1                                 tcaactTCTGTGGTGGGACCCACACCCCGACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACAAAAAAAAAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATA                             <  2:918816/135‑1                                         ttTGTTGGGGCCC‑CGCCCCAACTCGCATTGCCTGTAGAATTCCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAAAAAAAAAAAAAAAAGCTTATTACAAGCGCATTTTCGTTCAGTCAATTACTGCCAATATAACTTCGT                    <  2:1039849/139‑1                                                            CAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGAATAAAAAAGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAT  <  2:405163/141‑1                                                                                                                |||||||||||||                                                                             CAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTATGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/848470‑848580 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAT  >  USA300TCH1516_ALE/2866847‑2866922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.