New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2753848	168 (1.090)	8 (0.070) +ATACTTATAAAATTCAAAATCTTATGCATCATTA	8/200	15.3	6.0%	intergenic (+129/+59)	opcR/gloB	HTH‑type transcriptional repressor OpcR/Hydroxyacylglutathione hydrolase
	?	USA300TCH1516_ALE	2754851 =	169 (1.100)					intergenic (‑258/+6)	gloB/opuD_3	Hydroxyacylglutathione hydrolase/Glycine betaine transporter OpuD
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAACGACAATGATGATTATGCATGATAAAAACAATGCAATAGGTCCACGAAATAAACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2753732‑2753848 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTCAAGTTTAATTCTATCGCGCCCTAAAATGATTAAAAA  >  USA300TCH1516_ALE/2754851‑2754982                                                                                                                      ||||||||||||||||||||||||||||||||||                                                                                                                                     cagcggCAATGATGATTATGCATGATGAAAACAATACAATAGGTCCACGAAATAAACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTA                                                                                                                                                >  1:319972/7‑141                  ATGCATGATGAAAACAATACAATAGGTCCACGAAATAAACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAAT                                                                                                                               <  2:319972/141‑1                                             CCACGAAATAAACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCT                                                                                                    <  1:4731/141‑1                                                       AACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTATTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAA                                                                                          >  2:213783/1‑141                                                                       TCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACG                                                                          >  2:282713/1‑141                                                                                AGAAATTACCGTTTTTGTTTTATATGACAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAAC                                                                 >  1:375957/1‑141                                                                                     TTACCGTTTTTTTTTTTTTTTTCAATCAAATATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTT                                                            >  2:260394/1‑141                                                                                                           CAATCAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCCATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTC                                      <  2:830875/141‑1                                                                                                               CAATTATATACTTATAAAATTCAAAATCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTCAAGT                                  <  4:510194/141‑1                                                                                                                                         TCTTATGCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTCAAGTTTAATTCTATCGCGCCCTAAAATGAT        >  1:727357/1‑141                                                                                                                                               GCATCATTATTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTCAAGTTTAATTCTATCGCGCCCTAAAATGATTAAAAA  <  1:282713/141‑1                                                                                                                      ||||||||||||||||||||||||||||||||||                                                                                                                                     CAACGACAATGATGATTATGCATGATAAAAACAATGCAATAGGTCCACGAAATAAACGGTAATTTCTATCTCAATAAATAGAAATTACCGTTTTTGTTTTATATGACAATCAATTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2753732‑2753848 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTTGAATTATAAATTATCGTCTTGTTCTTCTTCTGATACTTGAACGATTCGCAATGAACGACGTTCAACTTCTTTTAATTTTTCAGCACGCGTTTCAAGTTTAATTCTATCGCGCCCTAAAATGATTAAAAA  >  USA300TCH1516_ALE/2754851‑2754982

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.