New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	34173 =	73 (1.250)	4 (0.070)	3/254	NT	5.1%	coding (462/480 nt)	rlmH	Ribosomal RNA large subunit methyltransferase H
	?	USA300TCH1516_ALE	= 88831	77 (1.350)					intergenic (+204/‑561)	nusG_1/USA300TCH1516_00080	Transcription termination/antitermination protein NusG/hypothetical protein

ACCTCATATGTTCTGATACATTCAAAATCCCTTTATGAAGCGGCTGAAAAAACCGCATCATTTATGATATGCTTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/34248‑34173 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tctGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTACACACTAAAAAATATCCTCCTTAACAATAATAAGTT  <  USA300TCH1516_ALE/88831‑88693                                                                                                                                                                                                                         ACCTCATATGTTCTGATACATTCAAAATCCCTTTATGAAGCGGCTGAAAAAACCGCATCATTTATGATATGCTTCTGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTT                                                                            <  2:356490/141‑1                             CCCTTTATGAAGCGGCTGAAAAAACCGCATCATTTATGATATGCTTCTGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCT                                                >  2:413873/1‑141                                                                  GATATGCTTCTGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTACACACTAAAAAATATCCTCCTTAACAA           >  1:6128/1‑141                                                                  GATATGCTTCTGCGTATCGGTAAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTAAACACTAAAAAATAACATCCTTAACAA           >  2:476795/1‑141                                                                           CTGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTACACACTAAAAAATATCCTCCTTAACAATAATAAGTT  >  1:287073/1‑141                                                                           CTGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTACACACTAAAAAATATCCTCCTTAACAATAATAAGTT  >  2:499714/1‑141                                                                                                                                                                                                                         ACCTCATATGTTCTGATACATTCAAAATCCCTTTATGAAGCGGCTGAAAAAACCGCATCATTTATGATATGCTTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/34248‑34173 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tctGCGTATCGGTTAATGATGCGGTTTTTAATTATATAATTTCAATTAATAAGGTAATGAACAGTTTTTTGATAAATGTTATTCTTCTAAAATTCTTTTTAATTTACACACTAAAAAATATCCTCCTTAACAATAATAAGTT  <  USA300TCH1516_ALE/88831‑88693

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