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

CTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGTA  >  USA300TCH1516_ALE/2086875‑2087155                                                                                                                                             |                                                                                                                                             cTAATTTATTTTAATGAATAAATAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCA                                                                                                                                              <  2:294967‑M1/141‑1 (MQ=255)  tAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCAc                                                                                                                                             <  1:304367/141‑1 (MQ=255)        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)                                             tCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCAccgaaatgcttacctttttttgtttttctataaatacaataagg                                                                                                  >  1:140033‑M1/1‑97 (MQ=255)                                             tCATTAACTACATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAAAAAAACAAAAAAAGATAAGCATTTCTGtgcttacttttttttgtttttctataaatacaataagt                                                                                                  <  2:140033‑M2/141‑39 (MQ=255)                                               aTTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACAt                                                                                                <  1:101671/141‑1 (MQ=255)                                               aTTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACAt                                                                                                <  1:102294/141‑1 (MQ=255)                                                  aaCTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCAccgaaaggcttacctttttttgtttttctataaatacaataagatatat                                                                                             >  1:198127‑M1/1‑92 (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)                                                                                                        actTATTGTATTTATAGAAAAACAAAAAAAAGTAAGCAcagaaatgcttatctttttttgtttttttataaatacaataaggtatgtcaatttgataatttattaattttcatttaataagaagatctatgtagttaatga                                       <  2:140033‑M1/140‑104 (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)                                                                                                                                       gTAAGCAtttcggtgcttacctttttttgtttttctataaatacaataaggtatgtcaatttgataatttattaattttcatttaataagaagatctatatagttaatgaataattaatgtacttttttttagtcagtcat        >  1:193815‑M1/1‑7 (MQ=255)                                                                                                                                            cACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGt   <  1:133584/141‑1 (MQ=255)                                                                                                                                             atttcggtgcttacctttttttgtttttctataaatacaataaggtatgtcaatttgataatttattaattttcatttaataagaagatctatatagttaatgaataattaatgtacttttttttagtcagtcattaaaat  <  1:11972‑M1/141‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             CTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAAACAATATAACACATATACATTGATTTGGAAAGCGCAAAAATAAATTTAATATACTAGCCCGAAGGGGAGCAATACATAAAAAATGAAAGGCGCTCCTTGAAAACGCCCAAGGTA  >  USA300TCH1516_ALE/2086875‑2087155

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.