New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2419897	90 (1.190)	5 (0.080)	4/228	NT	5.5%	intergenic (+65/‑172)	USA300HOU_RS12460/ssaA2_3	hypothetical protein/Staphylococcal secretory antigen ssaA2
	?	USA300TCH1516_ALE	= 2419903	92 (1.390)					intergenic (+71/‑166)	USA300HOU_RS12460/ssaA2_3	hypothetical protein/Staphylococcal secretory antigen ssaA2

ATTATCTTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2419745‑2419897 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aactttgactaattttGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACACACGCAATAAT  <  USA300TCH1516_ALE/2419903‑2419764                                                                                                                                                                                                                                                                                                        aaTATCTTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACT                                                                                                                                                           <  2:900985/139‑1      CTTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATTTCATTGTAACTTTGAC                                                                                                                                                      >  1:307709/1‑141       TTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACT                                                                                                                                                     >  1:298479/1‑141       TTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACT                                                                                                                                                     >  2:405812/1‑141       TTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTAATTGTAAGTTTGAtt                                                                                                                                                     >  1:352070/1‑139         TTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAA                                                                                                                                                   <  1:93359/141‑1             ATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTTTAACTTTGACTAATTTT                                                                                                                                               >  2:679632/1‑141                 ACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTTGTAA                                                                                                                                           >  1:738320/1‑141                 ACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTTGTAA                                                                                                                                           >  1:797980/1‑141                          GCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGAAACTTTGACTAATTTTGTAATA‑AAAATTA                                                                                                                                 >  2:255210/1‑141                                                                 CCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑TATTACAAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAA                                                                                          >  1:736540/1‑141                                                                                                ACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑TATTACAAAATTATTCAAAATTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCG                                                           >  2:797980/1‑141                                                                                                ACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑TATTACAAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCG                                                           >  2:738320/1‑141                                                                                                            TTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑TATTACAAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTACCATGTTTAAATAAATCGAATTGTTAAAGG                                               <  2:736540/141‑1                                                                                                                                          AACTTTGACTAATTTTGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTT                 >  2:682217/1‑141                                                                                                                                          AACTTTGACCAATTTTGTAATA‑AAAATTAGTCAAAGTTACAATGTGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTT                 >  2:485879/1‑141                                                                                                                                              TTGACTAATTTTGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAGTATGTTTAAATAAATCGAATTGTTAAATGTATTATATATTCTTGGCCATTATATTATTTGACA             >  1:509890/1‑141                                                                                                                                               TGACTAATTTTGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACAC            >  1:405812/1‑141                                                                                                                                                   tatgTTTGTAATA‑AATATTAGTCAAAGTTACAATGAGATTAACATATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACACACGC        <  1:255210/137‑1                                                                                                                                                    AATTTTGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACACACGCA       <  2:71408/141‑1                                                                                                                                                         TGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACACACGCAATAAT  <  1:347091/141‑1                                                                                                                                                                                                                                                                                                        ATTATCTTTTGTATTCACAATTATTGCGTGTGTCAAATATTATAATGGCCAAGAATATATAATACCTTTAACAATTCGATTTATTTAAACATATTACAAATAAATATTTCCTATTAATTATCTGTTAATCTCATTGTAACTTTGACTAATTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2419745‑2419897 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aactttgactaattttGTAATA‑AAAATTAGTCAAAGTTACAATGAGATTAACAGATAATTAATAGGAAATATTTATTTGTAATATGTTTAAATAAATCGAATTGTTAAAGGTATTATATATTCTTGGCCATTATAATATTTGACACACGCAATAAT  <  USA300TCH1516_ALE/2419903‑2419764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.