New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2087015	25 (0.770)	3 (0.100)	3/242	NT	11.3%	intergenic (‑166/‑519)	scn_3/chp	Staphylococcal complement inhibitor/Chemotaxis inhibitory protein
	?	USA300TCH1516_ALE	= 2087021	24 (0.800)					intergenic (‑172/‑513)	scn_3/chp	Staphylococcal complement inhibitor/Chemotaxis inhibitory protein

ATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGT  >  USA300TCH1516_ALE/2086882‑2087154                                                                                                                                            |                                                                                                                                      aTTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAAt                                                                                                                                      <  1:11972‑M2/141‑2 (MQ=255)       aTGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAAtgcttac                                                                                                                                >  1:193815‑M2/1‑134 (MQ=255)            tgactAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTATTATTAAGTGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACt                                                                                                                           <  1:392319/141‑1 (MQ=255)            tgaatAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACt                                                                                                                           <  1:276733/141‑1 (MQ=255)                  aaaaaaaGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCAt                                                                                                                     >  1:65642/1‑141 (MQ=255)                      aaaGTACATTAATTAATCATTAAATATATAGATCTTCTAATTAAATAAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAAc                                                                                                                 <  2:231072/141‑1 (MQ=255)                      aaaGTACAGTAATTATGAAGGAACTATATGGTTCTGCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAAc                                                                                                                 <  2:132960/141‑1 (MQ=255)                       aaGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACa                                                                                                                >  2:72606/1‑141 (MQ=255)                        aGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACaa                                                                                                               <  2:207190/141‑1 (MQ=255)                                      tCATTAACTACATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAAAAAAACAAAAAAAGATAAGCATTTCTGtgcttacttttttttgtttttctataaatacaataagt                                                                                                 <  2:140033‑M2/141‑39 (MQ=255)                                        aTTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACAt                                                                                               <  1:101671/141‑1 (MQ=255)                                        aTTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACAt                                                                                               <  1:102294/141‑1 (MQ=255)                                                 ataGATCTTCTTATTAAATGAACATTGATCAATAATCAAATTAACATACCTTATTGTATTTATAGAAAAACAAAAAAAGATAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTAGa                                                                                      >  2:123646/1‑141 (MQ=255)                                                 ataGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGa                                                                                      >  1:263996/1‑141 (MQ=255)                                                      tcttctTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAgcg                                                                                 >  1:112682/1‑141 (MQ=255)                                                             attaAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGCTTTGGACAGCGCAAaaat                                                                          >  2:301625/1‑141 (MQ=255)                                                             attaAATGAAAATTAATAAAATAGGAAATTGACATATCTTATTGTATTTATAGAAAAACAAAAAAAAGTAACCACCGAAATGCTTACCTACTTCACATAAACAATATAACACACATAAAATAATTTAGACAGCGCaaaaaa                                                                          >  2:144260/1‑140 (MQ=255)                                                                 aaTGAAAATTAATAAATTATCAAATTGACATACCCTATTGTATCTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAaaataaat                                                                      <  1:204613/141‑1 (MQ=255)                                                                     aaaaTTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTaa                                                                  >  1:224382/1‑141 (MQ=255)                                                                                atcataaaaTTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATCTCTTGGCAAACCGTTAATTTAAATTTAATATACTAGccc                                                       <  1:171800/135‑1 (MQ=255)                                                                                            atatatctTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCCTTTCGGtgcttacctttttttgtttttctataaatacaataaggtatgtcaatttgataatttattaattttcatttaataagaagatctatatagtt                                           >  1:198127‑M2/3‑49 (MQ=255)                                                                                                aCCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCGACTTCAACTAAACAATAGAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACa                                       >  1:291708/1‑141 (MQ=255)                                                                                                 ccTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCATTTCGGtgcttacctttttttgtttttctataaatacaataaggtatgtcaatttgataatttattaattttcatttaataagaagatctatatagttaatga                                      >  1:140033‑M2/1‑44 (MQ=255)                                                                                                                     aaCAAAAAAAGGTAAGCCCAGAAGTTCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCt                  <  2:361953/141‑1 (MQ=255)                                                                                                                      aaaaaaaaaGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCtt                 <  2:168005/139‑1 (MQ=255)                                                                                                                        aaaaaaaGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAACTGAAAAACTCTCCttaa               >  2:42195/1‑139 (MQ=255)                                                                                                                         aaaaaaGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACCTTGATTTTGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGaa              <  2:240451/141‑1 (MQ=255)                                                                                                                          aaaaaGGTAAGCACCGAAATGCTTACCTACTTGCCATAGACAATAGAACGCATAGACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGaaa             <  2:107862/141‑1 (MQ=255)                                                                                                                            aagggTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAAc           <  2:32054/138‑1 (MQ=255)                                                                                                                               ggTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATAAAAAAAAGATGAAAGGCGCTCCTTGCAAACGcc        >  1:72183/1‑141 (MQ=255)                                                                                                                                     cACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGt  <  1:133584/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                      ATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGT  >  USA300TCH1516_ALE/2086882‑2087154

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.