Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	1,909,272	Δ48 bp	28.0%	coding (79‑126/303 nt)	USA300HOU_RS09460 →	hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1909271	18 (0.590)	7 (0.230)	7/258	NT	28.0%	coding (78/303 nt)	USA300HOU_RS09460	hypothetical protein
	?	USA300TCH1516_ALE	1909320 =	18 (0.590)					coding (127/303 nt)	USA300HOU_RS09460	hypothetical protein

GTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1909165‑1909271 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTAT  >  USA300TCH1516_ALE/1909320‑1909450                                                                                                                                                                                                                                                GTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTATAACCTATCTAGCTTAATGATTATTTTAAGCTGTTTCTTNAATAGAAATAACATTAGTGGTATTAACGCNATTGTACTAATGTTGGCT                                                                                                    >  1:296748/1‑140         TAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTT                                                                                            <  1:287122/140‑1                     AGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTC                                                                                >  1:221500/1‑140                       cTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAA                                                                              <  1:256440/139‑1                                              AATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCA                                                       <  2:116939/140‑1                                                            TCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAAT                                         >  2:200163/1‑140                                                                                                   AATAACGTTAGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAACTGCGAGTAAAAGTTTGCCTAAGATTATTCTTATTGTTAT  >  1:99741/1‑140                                                                                                                                                                                                                                                GTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1909165‑1909271 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGTGTTATTAACTCAATTGTACTAATTTTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTAT  >  USA300TCH1516_ALE/1909320‑1909450

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.