New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1789630 =	12 (0.600)	3 (0.160)	3/238	NT	25.0%	intergenic (‑111/+59)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase
	?	USA300TCH1516_ALE	1789673 =	7 (0.380)					intergenic (‑154/+16)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase

CATTAATTGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTT  >  USA300TCH1516_ALE/1789495‑1789759                                                                                                                                         |                                                                                                                                  cATTAATTGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGCATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAACAACTATTCAt                                                                                                                              >  2:163074/1‑141 (MQ=255)                    tGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAAcgc                                                                                                           >  2:130330/1‑141 (MQ=255)                    tGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAAcgc                                                                                                           >  2:130335/1‑141 (MQ=255)                           aaaaGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGAG‑CCAGTGATGATGGTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGcgtacgta                                                                                                    >  1:57601/1‑141 (MQ=255)                               gCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGAATAATAGAGGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGt                                                                                                >  1:208060/1‑141 (MQ=255)                                           ttttATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTTCTTACATACATCAACGCGTACGTAAAGTAATGACttattt                                                                                    <  2:209247/140‑1 (MQ=255)                                                 gtgtTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATATATCAACGCGTACGTAAAGTAATTACTTATTTATAgtt                                                                              >  2:230688/1‑140 (MQ=255)                                                      ataCTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAata                                                                         <  2:139970/141‑1 (MQ=255)                                                       aaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAATCATTACTTACATACATCAACGCGTACGTAAAGAAATGACTTATTATAAGTGTAata                                                                         <  2:82008‑M1/59‑1 (MQ=255)                                                                             atatTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCg                                                  <  2:150343/141‑1 (MQ=255)                                                                                                         cggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTCATCCTTCTTTTCAATATAACCttcttcttctt                       <  2:99005‑M1/109‑2 (MQ=255)                                                                                                                      tatCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAg          <  2:57601/141‑1 (MQ=255)                                                                                                                         tattacactataaataATTCATTACTTACATACATCAACGCTTACGTATAGTAATGACTTATTTATAGTGTAATATTAATTTTCTTTTTCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt       >  1:82008‑M1/17‑141 (MQ=255)                                                                                                                              ttATAAAAAATAGTCGTTTAGAAAGCACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgtt  >  2:55002/1‑141 (MQ=255)                                                                                                                              ttATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTTGAACAATCTATCAAAgttttatt  >  2:143619/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                  CATTAATTGCAATATTCGTTGACATTAAAAGCACCCCTTGATCTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGAT‑TTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTT  >  USA300TCH1516_ALE/1789495‑1789759

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.