New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2746384	46 (1.000)	4 (0.090)	4/244	NT	8.2%	intergenic (‑632/+53)	mqo2/acsA_2	putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase
	?	USA300TCH1516_ALE	= 2746433	46 (1.060)					intergenic (‑681/+4)	mqo2/acsA_2	putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase

AATGCCGGTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2746237‑2746384 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aataaacaTAGCAAAGCAGTCCAATGCGTAAGGTATGATGATACGCACTGGACTGCTTGTTTATTTATGATGTTCTTTGTCGTCTAGTTATAAATATTAAAATTAGTTTAGAAACAAGCGCAACCAGTATTAAGAATGAGAAAATA  <  USA300TCH1516_ALE/2746433‑2746296                                                                                                                                                                                                                                                                                                AATGCCGGTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAA                                                                                                                                                   >  1:699299/1‑141       GGTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAAC                                                                                                                                             <  1:577522/141‑1        GTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA                                                                                                                                            <  1:639600/141‑1        GTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATCTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA                                                                                                                                            >  1:714237/1‑141                                         TTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACATAGCAAAGCAGTCCAATGCGTAAGGTATGATGA                                                                                                           <  2:282785/141‑1                                         TTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAAC‑‑‑‑‑‑AAGCAGTCCAATGCGTAAGGTATGATGATACGCA                                                                                                     <  2:226060/141‑1                                                                     ATTCTTCATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAACAACATCATAAATAAACATCGCAAAGCAGTCCAATGCGTAAGGTATGATGATACGCACTGGACTGCTTGTTTATTTATG                                                                               <  1:197024/141‑1                                                                                 GGTTGCGCTTATTTCTAAACTAATTTTAATTTTTATAACTAGACGACAAAGAACATCATAAATAAAC‑‑‑‑‑‑AAGCAGTCCAATGCGTAAGGTATGATGATACGCACTGGACTGCTTGTTTATTTATGATGTTCTTTGTCGTCTAG                                                             <  1:630947/141‑1                                                                                                                                                  ACATAGCAAAGCAGTCCAATGCGTAAGGTATGATGCTACGCACTGGACTGCTTGTTTATCTATGATGTGCTTTGTCGTCTAGTTATAAATATTAAAATTAGTTTAGAAACAAGCGCAACCAGTATTAAGAATGAGAAAATA  <  2:64344/141‑1                                                                                                                                                                                                                                                                                                AATGCCGGTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2746237‑2746384 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aataaacaTAGCAAAGCAGTCCAATGCGTAAGGTATGATGATACGCACTGGACTGCTTGTTTATTTATGATGTTCTTTGTCGTCTAGTTATAAATATTAAAATTAGTTTAGAAACAAGCGCAACCAGTATTAAGAATGAGAAAATA  <  USA300TCH1516_ALE/2746433‑2746296

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