New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 557240	NA (NA)	3 (0.050)	3/250	NT	NA	intergenic (+298/‑1471)	USA300TCH1516_00504/USA300TCH1516_00505	tRNA‑Ala/tRNA‑Ile
	?	USA300TCH1516_ALE	= 557277	NA (NA)					intergenic (+335/‑1434)	USA300TCH1516_00504/USA300TCH1516_00505	tRNA‑Ala/tRNA‑Ile

GCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/557099‑557240 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑accgTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTAACATCAGAGAAGCAAGCTTCTCG  <  USA300TCH1516_ALE/557277‑557139                                                                                                                                                                                                                                                                                           GCTGGCGGCGTGCCTAATACGTGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATAC                                                                                                                                               >  2:55905/1‑140  CTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACC                                                                                                                                              >  1:48660/1‑140   tcgaGGCGTGCCTAAAACATGAAAGACAGGCTAAGCGGCGAGAAGCTTGCTTTTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCG                                                                                                                                             <  1:714757/136‑1   TGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCG                                                                                                                                             <  1:357657/140‑1   TGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACGTCGGGAAGCCGGAGCTAATACCG                                                                                                                                             >  2:389043/1‑140         CGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGTCTTTC                                                                                                                                       >  2:452215/1‑140                                      ggtCGAGAAGCTTGCTTTTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGTCTTTCACTTTTGAACCATGCGGTTCAAAATATTA                                                                                                          <  1:77729/137‑1                                         CGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCC                                                                                                       <  1:452215/140‑1                                                                                                                                      tcaacACCGTCTTTCACTTTTTACCCTTGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCTGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTAACATCAGAGAAGCAA          <  2:692278/135‑1                                                                                                                                            CCGTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCGCGTGTTACTCACCCGTCCGCCGCTAACATCAGAGAAGCAAGCTTCT    >  1:77659/1‑140                                                                                                                                            CCGTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTGACATCAGACAAGCAAGCTTCT    >  1:57924/1‑140                                                                                                                                              GTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCTCGTGTTACTCACCCGTCCGCCGCTATCATCAGAGAAGCAAGCTTCTCG  >  1:297386/1‑140                                                                                                                                              GTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTAACATCAGAGAAGCAAGCTccccg  >  2:27209/1‑135                                                                                                                                              GTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATACCAGTCTTATAGGTAGGTTATCCACGTGCTACTCACCCGTCAGCCGCTAACATCAGAGAAGCACGCTGCTCG  >  2:374314/1‑140                                                                                                                                              GTCTTTCACTTTTCACCTGTGCGGTCCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTAACATCAGACAAGCAAGCTTCTCG  <  1:491572/140‑1                                                                                                                                                                                                                                                                                           GCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/557099‑557240 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑accgTCTTTCACTTTTGAACCATGCGGTTCAAAATATTATCCGGTATTAGCTCCGGTTTCCCGAAGTTATCCCAGTCTTATAGGTAGGTTATCCACGTGTTACTCACCCGTCCGCCGCTAACATCAGAGAAGCAAGCTTCTCG  <  USA300TCH1516_ALE/557277‑557139

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.