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

CTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGATCGGCCATTCGG  >  USA300TCH1516_ALE/1789537‑1789809                                                                                                                                         |                                                                                                                                         ttttATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTTCTTACATACATCAACGCGTACGTAAAGTAATGACttattt                                                                                                                                      <  2:209247/140‑1 (MQ=255)       gtgtTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATATATCAACGCGTACGTAAAGTAATTACTTATTTATAgtt                                                                                                                                >  2:230688/1‑140 (MQ=255)            ataCTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAata                                                                                                                           <  2:139970/141‑1 (MQ=255)            aaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacggagaagaagattaatattacactataaataAATCATTACTTACATACATCAACGCGTACGTAAAGAAATGACTTATTATAAGTGTAata                                                                                                                           <  2:82008‑M1/59‑1 (MQ=255)            aaccttgagagattgttagaagaagaaggttatattgaaaagccgaattacgaaaaagaaaattaatattacactataaataagtcattactatacgtaagcgttgatgtatgtaagtaatgaatTATTTATAGTGTAata                                                                                                                           >  1:82008‑M2/126‑141 (MQ=255)                            aagaagaagaaggttatattgaaaagaaggatgacggagaagaagattaatattacactataaataagtcattactttacgtacgcgttgatgtatgtaagtaatgactTATTTATAGTGTAATATTAATCTTCTTCTCCg                                                                                                           <  2:99005‑M2/32‑1 (MQ=255)                                   atatTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCg                                                                                                    <  2:150343/141‑1 (MQ=255)                                                              cggagaagaagattaatattacactataaataAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTCATCCTTCTTTTCAATATAACCttcttcttctt                                                                         <  2:99005‑M1/109‑2 (MQ=255)                                                                           tatCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAg                                                            <  2:57601/141‑1 (MQ=255)                                                                              tattacacttataataagtcatttctttacgtacgcgttgatgtatgtaagtaatgattTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt                                                         <  2:82008‑M2/82‑1 (MQ=255)                                                                              tattacactataaataATTCATTACTTACATACATCAACGCTTACGTATAGTAATGACTTATTTATAGTGTAATATTAATTTTCTTTTTCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgtt                                                         >  1:82008‑M1/17‑141 (MQ=255)                                                                                   ttATAAAAAATAGTCGTTTAGAAAGCACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGgttttgtt                                                    >  2:55002/1‑141 (MQ=255)                                                                                   ttATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTTGAACAATCTATCAAAgttttatt                                                    >  2:143619/1‑141 (MQ=255)                                                                                                                   aCGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCTCATTAATTATCGATa                    >  2:147370/1‑141 (MQ=255)                                                                                                                          cgtaAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCGAAATTATCGATAACATGAt             <  1:130093/141‑1 (MQ=255)                                                                                                                                     gACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAGCCCTCTTCTTCTAACAATCTCTCAAAGATTATTGTGATGTCACTTTTATACCCTAAATTATTCATAACATTATCTGCCATTctg  >  2:148449/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                         CTTTATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTACATACATCAACGCGTACGTAAAGTAATGACTTATTTATAGTGTAATATTAATCTTCTTCTCCGTAATTCGGCTTTTCAATATAACCTTCTTCTTCTAACAATCTCTCAAGGTTTTGTTTTAATTCAAGTTTATCCCCTAAATTATCGATAACATGATCGGCCATTCGG  >  USA300TCH1516_ALE/1789537‑1789809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.