New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1789640	81 (0.820)	5 (0.060)	5/138	NT	6.8%	intergenic (‑121/+49)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase
	?	USA300TCH1516_ALE	= 1789661	67 (0.790)					intergenic (‑142/+28)	gapA2/coaE	Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase

TATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1789540‑1789640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcattacttTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATATAA  <  USA300TCH1516_ALE/1789661‑1789574                                                                                                                                                                                               TATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATA                                                                                                    >  1:1695584/1‑91  ATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAG                                                                                                   <  1:3161842/91‑1  ATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAG                                                                                                   >  1:1839642/1‑91   TGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGT                                                                                                  <  1:152193/91‑1   TGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGT                                                                                                  >  1:885324/1‑91    GTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTC                                                                                                 <  1:1823781/91‑1    GTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTC                                                                                                 <  1:2033887/91‑1    GTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTC                                                                                                 <  1:2032709/91‑1      GTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCAT                                                                                               <  1:1796779/91‑1      GTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCAT                                                                                               <  1:3118388/91‑1      GTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCAT                                                                                               >  1:2011073/1‑91      GTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGCTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCAT                                                                                               >  1:2010953/1‑91       TTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATT                                                                                              >  1:2968953/1‑91                                  ATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTTACGTACGCGTTGATGTATGTAA                                                                   <  1:987441/91‑1                                   TTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTTACGTACGCGTTGATGTATGTAAG                                                                  <  1:1493484/91‑1                                             TTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTAT                                                        <  1:1812436/91‑1                                                     CGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATGACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATA                                                <  1:3296190/91‑1                                                            CGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGA                                         <  1:2029618/91‑1                                                                                           AGTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATT          >  1:2530086/1‑91                                                                                            GTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTT         <  1:1831697/91‑1                                                                                            GTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTT         >  1:2134030/1‑91                                                                                            GTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTT         <  1:1830805/91‑1                                                                                            GTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTT         >  1:1551710/1‑91                                                                                            GTCATTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTT         >  1:1551582/1‑91                                                                                                TTACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATA     <  1:3083231/91‑1                                                                                                 TACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATAT    <  1:3633376/91‑1                                                                                                 TACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATAT    >  1:3748523/1‑91                                                                                                 TACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATAT    <  1:3798832/91‑1                                                                                                 TACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATAT    >  1:1251053/1‑91                                                                                                  ACTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATATA   >  1:198005/1‑91                                                                                                   CTTTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATATAA  <  1:2492473/91‑1                                                                                                                                                                                               TATGTGTTATACTTTATGGAATTAGTATAGCATATTATATGAAATTTGAAAGCGTTTTCCGTTGATTTATTTATCTTTTTTATAAAAAATAGTCATTACTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1789540‑1789640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcattacttTACGTACGCGTTGATGTATGTAAGTAATGACTATTTTTTATAAAAAAGATAAATAAATCAACGGAAAACGCTTTCAAATTTCATATAA  <  USA300TCH1516_ALE/1789661‑1789574

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