New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2001491 =	11 (0.180)	3 (0.050)	3/244	NT	22.4%	intergenic (‑3219/+116)	USA300TCH1516_01882/USA300TCH1516_01883	tRNA‑Val/tRNA‑Ala
	?	USA300TCH1516_ALE	2179606 =	NA (NA)					intergenic (+3368/+1927)	ilvA/USA300TCH1516_02069	L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly

CAGCGGTTCGATCCCGCTAGTCTCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2001635‑2001491 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtgttcTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCGC  >  USA300TCH1516_ALE/2179606‑2179744                                                                                                                                                                                                                                                                                              CAGCGGTTCGATCCCGCTAGTCTCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAG                                                                                                                                                  >  1:420385/1‑140    ccGTTCGATCCCGCTAGTTCCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCTAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGT                                                                                                                                               <  2:179566/138‑1                       TCCACCATTATTTGTACATTGAAAACTTGATAAGTAACTAAAATATAGATTGTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGTAATAATCGCTAGTGTTCTTTCGAACACTAGCGAT                                                                                                                            <  2:435506/140‑1                                                                                             GAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTAGCGATTATTTCTTATGAATACAAGCTTATTTAAAACTCTTTATTAACTCGATTTTGCTTGTTAAAATCTATATTT                                                      >  1:15305/1‑140                                                                                                    GAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTAGCGATTATTTCTTATGAATTATAGAGTTATTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTAC                                               >  1:712630/1‑140                                                                                                                                      ttgtTAGTGTTCTTTCGCACAATAGCCATTTTTTCTTATCAATTCAATCTTATTTAAACCTCTTTATTGACTCGGCTTTGCTTGGTAAAAGCTATAGTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGT             <  2:605817/136‑1                                                                                                                                      ttgggtGTGTTCTTTCGAACACTAGCGATTATTTCTTATGATTTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGT             <  1:81814/134‑1                                                                                                                                            GTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCG       >  1:565406/1‑140                                                                                                                                            GTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCG       >  1:395715/1‑140                                                                                                                                            GTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTAATTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTATAAATGTACTATTTCTTTTTAGTCTAGCG       >  2:463333/1‑140                                                                                                                                             TGTTCTTTCGATCACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGC      <  2:297186/140‑1                                                                                                                                             TGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGC      <  1:50184/140‑1                                                                                                                                             TGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGC      <  1:250259/140‑1                                                                                                                                                TCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTCGACTGGGGAATTTACTTAATTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCG   >  1:166532/1‑140                                                                                                                                                TCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCG   >  2:109607/1‑140                                                                                                                                                TCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCG   <  2:573458/140‑1                                                                                                                                                TCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTAGTAATTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCCATGTACAATTTCTTTTTAGTTAAGCTCTCt   >  1:351255/1‑139                                                                                                                                                 CTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTAACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCGC  >  2:573992/1‑140                                                                                                                                                                                                                                                                                              CAGCGGTTCGATCCCGCTAGTCTCCACCATTATTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2001635‑2001491 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtgttcTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAATTTCTTTTTAGTCAAGCGCTCGC  >  USA300TCH1516_ALE/2179606‑2179744

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.