New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1676788	167 (0.820)	15 (0.080)	8/156	NT	8.7%	intergenic (‑344/‑75)	ccpN/glyQS	Transcriptional repressor CcpN/Glycine‑‑tRNA ligase
	?	USA300TCH1516_ALE	= 1676835	154 (0.780)					intergenic (‑391/‑28)	ccpN/glyQS	Transcriptional repressor CcpN/Glycine‑‑tRNA ligase

AATAAAAGCGAGTGACTACACTAATTTGGGTGGAACCGCGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1676697‑1676788 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTACG  <  USA300TCH1516_ALE/1676835‑1676746                                                                                                                                                                                        AATAAAAGCGAGTGACTACACTAATTTGGGTGGAACCGCGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTC                                                                                             <  1:2386681/91‑1                                     CGCGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTT                                                         <  2:3264929/91‑1                                      GCGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGTCCCATGGAAAATAACAGCATAGTAAATATGCTTTA                                                        <  2:672732/91‑1                                       CGGGTTGAAGAGGTAACTTATGTTGTATTATATACAATTTAAGATATTAACTCGCCCCATGGAAAATAACAGCATAGTCAATATGCTTTAC                                                       <  2:2664253/91‑1                                       CGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTAC                                                       <  2:123618/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGTCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  2:2702703/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGTCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  1:2602455/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGTCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  1:2602370/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  1:387941/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  1:1851882/91‑1                                        GGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACT                                                      <  2:138237/91‑1                                         GGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTT                                                     <  2:3184734/91‑1                                          GTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTC                                                    <  1:2071543/91‑1                                           TTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCC                                                   <  1:482146/91‑1                                           TTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCC                                                   <  2:1335208/91‑1                                                             TTGTATTATATACAATTTAAAATATTAACTCGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATT                                 <  1:1139153/91‑1                                                                                           CGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTAC   >  1:1438651/1‑91                                                                                           CGCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTAC   >  1:1562434/1‑91                                                                                            GCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTACG  <  1:3950503/91‑1                                                                                            GCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTACG  <  1:366488/91‑1                                                                                                                                                                                        AATAAAAGCGAGTGACTACACTAATTTGGGTGGAACCGCGGGTTAAATACGTAACTTATTTTGTATTATATACAATTTAAAATATTAACTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1676697‑1676788 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgCCCCATGGAAAATAACAGCATAGTAAATATGCTTTACTTCCATGGGACGAGTTAATATTTTAAATTGTATATAATACAAAATAAGTTACG  <  USA300TCH1516_ALE/1676835‑1676746

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