Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	130,854	(T)5→1	14.4%	intergenic (‑94/+272)	sarS ← / ← yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 130853	65 (1.150)	11 (0.200)	8/256	NT	14.4%	intergenic (‑93/+276)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA
	?	USA300TCH1516_ALE	130858 =	66 (1.180)					intergenic (‑98/+271)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

ATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/130717‑130853 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGA  >  USA300TCH1516_ALE/130858‑130954                                                                                                                                                                                                                                            ATGATTATAAAATCTCTAATTTTGTTATGGTGAATATAGTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATT                                                                                                >  2:152838/1‑140                                    ATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATAATATATTAAAATATGTGTTTTTGAATAAATGACATTATTAAA                                                             >  2:112428/1‑140                                                  TATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAAT                                               <  2:381728/140‑1                                                                           TTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAA                      <  1:77886/140‑1                                                                              ATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATTGATATTTGAAAAct                   >  2:598897/1‑138                                                                              ATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAAT                   >  2:150866/1‑140                                                                                tTAACACCATATAATATAAAAAACAATCCATAAGTTATAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGACGAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCG                 <  2:447782/139‑1                                                                                  AACACAATATAATAAGAAAAATCATCCATAATTTACAATTACCACGCGCGCGATATATTAACATTTGAGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAA               >  2:316219/1‑140                                                                                    CACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGA             >  1:637324/1‑140                                                                                    CACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGA             >  1:660994/1‑140                                                                                               AAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATAAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGA  <  1:462467/140‑1                                                                                               AAGAAAAATAAGCCATAATTTACAATTAAAAATAATATGATATATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGA  <  1:147584/140‑1                                                                                                                                                                                                                                            ATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/130717‑130853 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGA  >  USA300TCH1516_ALE/130858‑130954

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.