New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2054896 =	41 (0.800)	4 (0.080)	4/248	NT	9.5%	intergenic (‑37/‑824)	purB/sspP	Adenylosuccinate lyase/Staphopain A
	?	USA300TCH1516_ALE	2054942 =	37 (0.760)					intergenic (‑83/‑778)	purB/sspP	Adenylosuccinate lyase/Staphopain A

AGCGATTTTGATCAGTCCAAATATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCTAATTGTAAATGTTCGCAAT  >  USA300TCH1516_ALE/2054802‑2055082                                                                                                                                             |                                                                                                                                             aGCGACTTTGATCAGTCCAAATATTGGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTa                                                                                                                                              <  1:600324/141‑1 (MQ=255)     aTTTTGATCAGTCCAAATATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAactc                                                                                                                                          >  2:612404/1‑141 (MQ=255)           aTCAGTCCAAATATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAactctactct                                                                                                                                    >  1:98241/1‑141 (MQ=255)              aaaaaataaaatagaatgagaatatacggaaattttttatacatatatatgcaaagatataaaaatgtgaagagtaaagttaaaaacgaactttttgtttatttttattaaaaaatgtactgtttttAACTCTACTCTTca                                                                                                                                 >  1:179199‑M2/128‑141 (MQ=255)              aGTCCAAATATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTca                                                                                                                                 <  1:129058/141‑1 (MQ=255)                    aaTATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGttt                                                                                                                           >  1:590252/1‑141 (MQ=255)                      tatTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTaa                                                                                                                         >  2:326013/1‑141 (MQ=255)                      tatTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTaa                                                                                                                         <  1:320233/141‑1 (MQ=255)                      aaatagaatgagaatatacggaaattttttatacatttataaccaattctgttaaactgtgaagagtagagttAAAAACAGAACATTTTTTAATAAAAATAAAAAAAAAATTCGTTTTTAACTCTACTTTTTACAGTTTaa                                                                                                                         <  2:354978‑M1/68‑1 (MQ=255)                      aaatagaatgagaatatacggaaattttttatacatttataacaaattctgttaaagtgtgaagagtagaaataaaaacgaactttttatttatttttattaaaaaattttgtgtttttAACACTACTATAAACAGTTTaa                                                                                                                         >  1:354978‑M2/120‑141 (MQ=255)                       atTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAACCAGTTAGTTTTTAACTCTTCTCTTCACAGTTTAAc                                                                                                                        <  1:154691/141‑1 (MQ=255)                       atTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAAc                                                                                                                        <  1:28504/141‑1 (MQ=255)                         tAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACATCTTAACAg                                                                                                                      >  2:571619/1‑141 (MQ=255)                             atgagaatatacggaaattttttatacatttataaccaattctgttaaaatgtgaagagtagagttAAAAAAATAACATTTTTTAATAAAAATAAACAAAAAAATCGATATTAACTCTACTCTTCACAATTTAACAAAAtt                                                                                                                  <  2:433570‑M1/75‑1 (MQ=255)                               tgtcttttCTAGAATAGCGTTCAACAATTTTTTAAACTCATACCGTATGTATACTCGAATGTACAAAAACAAAAAATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTgg                                                                                                                <  2:107214/139‑1 (MQ=255)                                 tcttctCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCATCACAGTTTAACAGAATTGGtt                                                                                                              >  2:449590/1‑141 (MQ=255)                                   ttctCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTTTTTTTTTTTAACATAAAGTTCGTTTTTCACTCTACTTTTCACTGTTTAACAGTATTGGTtat                                                                                                            >  2:323008/1‑141 (MQ=255)                                   ttctCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTtat                                                                                                            >  2:261191/1‑141 (MQ=255)                                                cGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATaaaaa                                                                                               >  1:441589/1‑141 (MQ=255)                                                cGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATaaaaa                                                                                               >  1:519516/1‑141 (MQ=255)                                                cGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATaaaaa                                                                                               >  2:212887/1‑141 (MQ=255)                                                   tCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGTTTATAAATTTATATAAAAtt                                                                                            >  2:128708/1‑141 (MQ=255)                                                   tCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAAtt                                                                                            >  1:41169/1‑141 (MQ=255)                                                   tCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAAtt                                                                                            >  1:358655/1‑141 (MQ=255)                                                     aaTCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTc                                                                                          <  1:537239/141‑1 (MQ=255)                                                        cATTTTTTTAACTCCTATAGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAGGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGt                                                                                       <  2:604123/141‑1 (MQ=255)                                                           ttttttAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGtata                                                                                    >  2:241823/1‑141 (MQ=255)                                                           ttttttAAATCCGAACGGAAGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGtata                                                                                    <  1:194706/141‑1 (MQ=255)                                                             ttttAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATAtt                                                                                  <  2:31028/141‑1 (MQ=255)                                                                  aattttgttaaattgtgaagagtagagttaatatcgatttttttgtttatttttattaaaaaatgttatttttttAACTCTACTCTTCACATTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCAt                                                                             <  2:433570‑M2/66‑1 (MQ=255)                                                                       tATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtat                                                                        >  1:195715/1‑141 (MQ=255)                                                                         ttaaactgtttatagtagtgttAAAAACACAAAATTTTTTAATAAAAATAAATAAAAAGTTCGTTTTTATTTCTACTCTTCACACTTTAACAGAATTTGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtattt                                                                      >  1:354978‑M1/23‑141 (MQ=255)                                                                         ttaaactgtaaaaagtagagttaaaaacgaattttttttttatttttattaaaaaatgttctgtttttAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtattt                                                                      <  2:354978‑M2/73‑1 (MQ=255)                                                                         tCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtattt                                                                      <  1:163305/141‑1 (MQ=255)                                                                           gtatgtatACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAGTTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtatttta                                                                    <  1:559317/141‑1 (MQ=255)                                                                             atgtatACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATGACCAAAAAGTTTGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTCATAAATGTATAAAAAATTTCCGTATATTCTCTTTCtattttatt                                                                  >  2:457482/1‑141 (MQ=255)                                                                             atgtatACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtattttatt                                                                  >  2:502671/1‑141 (MQ=255)                                                                             atgtatACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCtattttatt                                                                  >  2:502694/1‑141 (MQ=255)                                                                                 tgaagagtagagttAAAAACAGTACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTTTACTCTTCACATTTTTATATCTTTGCATATATATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTAtttttt                                                              >  1:179199‑M1/15‑141 (MQ=255)                                                                                          ttttCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAAAAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCTTTCTATTTTATTTTTTACAttttta                                                     >  2:473300/1‑137 (MQ=255)                                                                                              cAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTAAATTAGTACAAt                                                 >  1:59643/1‑141 (MQ=255)                                                                                              cAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTAGTTTTTAACTCTACTCTTCACAGTTTAACAGATTTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTATATTAATatgat                                                 >  1:59589/1‑137 (MQ=255)                                                                                                      gAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATg                                         <  1:40715/141‑1 (MQ=255)                                                                                                                taataaAAATAAACAAAAAGTTCGTTTTTAACTCTCCTCATAACAACAGAACATAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAAt                               <  1:603285/141‑1 (MQ=255)                                                                                                                 aataaaaataaaCAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATa                              >  2:4414/1‑141 (MQ=255)                                                                                                                          aaaCAAAAACTTCCTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCTGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCt                     <  2:411/141‑1 (MQ=255)                                                                                                                           aaCAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCTa                    <  1:254180/141‑1 (MQ=255)                                                                                                                                       ttttttAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCTAATTGTAAATGtt        <  2:594499‑M2/135‑1 (MQ=255)                                                                                                                                             aaCTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCTAATTGTAAATGTTCGCAAt  >  1:156305/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             AGCGATTTTGATCAGTCCAAATATTAGACATTTCTTCTCTAGAATAGCGTTCAATCATTTTTTTAACTCCTATCGTATGTATACTCGAATTTTCAAAAACAGAACATTTTTTAATAAAAATAAACAAAAAGTTCGTTTTTAACTCTACTCTTCACAGTTTAACAGAATTGGTTATAAATGTATAAAAAATTTCCGTATATTCTCATTCTATTTTATTTTTTACATTAATACAATTATCTATGGCAGATTAATACTGATTTCTAATTGTAAATGTTCGCAAT  >  USA300TCH1516_ALE/2054802‑2055082

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.