New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1168782	226 (1.190)	9 (0.060)	4/124	NT	5.3%	intergenic (+638/+15)	scn_2/USA300HOU_RS05810	Staphylococcal complement inhibitor/hypothetical protein
	?	USA300TCH1516_ALE	= 2220770	146 (0.990)					intergenic (‑421/+141)	USA300HOU_RS11345/atpC	hypothetical protein/ATP synthase epsilon chain

TGATAAAGAACCACTACATAATAAATCATTAGTGGTTCTTTATCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1168736‑1168782 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagtggttctttatcattAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCTTT  <  USA300TCH1516_ALE/2220770‑2220681                                                                                                                                           TGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAA                                                >  1:1823746/1‑91    TAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACT                                             >  2:901895/1‑91     tAAGAACCACTACATAATAAATCATTAGTGGCTCTTAAACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTC                                            >  2:1096469/2‑91     tAAGAACCACTACATAATAAATCATTAGTGGCTCTTAAACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTC                                            >  2:1096453/2‑91       AGAACCACTACATAATAAATCATTAGTGGCTCTTAAACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCAT                                          >  1:3259298/1‑91          ACCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTA                                       >  1:302457/1‑91          ACCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTA                                       >  1:302827/1‑91           CCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTAT                                      >  1:3672422/1‑91           CCACTACATCATAAATCTTTAATGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTAT                                      >  1:3672286/1‑91                              TAGTGGTTCTTTATCATTAAACGCAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAA                   <  2:3124318/91‑1                              TAGTGGGTCTTTATCATTAAACGCAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAA                   <  2:3124331/91‑1                               AGTGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAA                  >  1:1707636/1‑91                               AGTGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAA                  >  1:1712096/1‑91                               AGTGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAA                  >  1:2203182/1‑91                                 gaaTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGA                >  2:1512550/4‑91                                 TGGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGA                <  2:2427168/91‑1                                  GGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAA               <  2:438960/91‑1                                  GGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAA               <  2:2495426/91‑1                                  GGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAA               <  2:984880/91‑1                                  GGTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAA               <  1:1041684/91‑1                                   GTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAA              >  1:2232968/1‑91                                   GTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAA              <  1:3676529/91‑1                                   GTTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAA              >  2:1888198/1‑91                                    TTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAA             >  2:3665922/1‑91                                    TTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAA             <  2:281938/91‑1                                    TTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAA             <  2:281502/91‑1                                    TTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAA             <  2:281271/91‑1                                    TTCTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAA             >  2:1767869/1‑91                                      CTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAG           >  2:2390333/1‑91                                      CTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAG           >  2:2024474/1‑91                                      CTTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAG           <  1:1255743/91‑1                                       TTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGT          >  2:1302229/1‑91                                       TTTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGT          >  2:162857/1‑91                                        TTATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTA         <  1:2627317/91‑1                                         TATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACAGGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTAT        <  2:74263/91‑1                                          ATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATT       <  1:2126215/91‑1                                          ATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATT       >  2:224228/1‑91                                          ATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATT       <  1:3854700/91‑1                                          ATCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATATATAAAGAAAAAGTATT       <  2:197533/91‑1                                           aCATTAAACACAGCTAATGTGTATGTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTT      <  2:3600338/90‑1                                           TCATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTT      <  1:218542/91‑1                                            CATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTC     <  1:622700/91‑1                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    <  1:416297/91‑1                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    >  1:2196/1‑91                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    <  1:3584872/91‑1                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    >  1:3640145/1‑91                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    <  2:1149055/91‑1                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    <  2:1175133/91‑1                                             ATTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCT    <  2:1500599/91‑1                                              TTAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCTT   <  2:1229853/91‑1                                               TAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCTTT  >  1:537690/1‑91                                                                                                                                           TGATAAAGAACCACTACATAATAAATCATTAGTGGTTCTTTATCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1168736‑1168782 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagtggttctttatcattAAACACAGCTAATGTGTATTTAAAAATAGGAATACATGAGTAAAACTCATGTATAAGAAATACTAATTTCTAAAGAAAAAGTATTTCTTT  <  USA300TCH1516_ALE/2220770‑2220681

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.