New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 45071624 (0.370)33 (0.590) 27/226 NT 63.6% intergenic (+83/‑281) speC_3/tst_2 Exotoxin type C/Toxic shock syndrome toxin‑1
?USA300TCH1516_ALE 451778 = 17 (0.300)intergenic (+77/‑369) tst_2/USA300HOU_RS02140 Toxic shock syndrome toxin‑1/hypothetical protein

ACAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/450564‑450716
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTGA  >  USA300TCH1516_ALE/451778‑451915
                                                                                                                                                                                                                                                                                                   
ACAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAACACAAGAAGTTAAGTGACAACGGCCTACATGTTGC                                                                                                                                                        >  2:726031/1‑141
 CAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCT                                                                                                                                                       >  1:311499/1‑141
 CAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCT                                                                                                                                                       >  2:478053/1‑141
 CAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAACTGACAACGGCCTACATGTTGCT                                                                                                                                                       >  1:691414/1‑141
        ATCGCATGGCAGATGACATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCGTAGCTTC                                                                                                                                                <  1:492342/141‑1
         TCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCT                                                                                                                                               <  1:76373/141‑1
          CGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTT                                                                                                                                              <  2:109015/141‑1
          CGCATGGCAGATGTCATAGATGGCACTAATATTCATAACATTGAAGTGAATATAACATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAACACAAGAAGTTAAGTGACAACGGCATACATGTTGCTTAGCTTCTT                                                                                                                                              <  2:433538/141‑1
            CATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTT                                                                                                                                            >  1:710142/1‑141
              TGGCAGATGTCATAGATGGCACTAATATTGATCACATTGAAGTGAATATAAAATAATCATGACAATCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGAAAACGGCCTACATGTTCCATAGCTTCATTTTT                                                                                                                                          >  2:118344/1‑141
                 CAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAAGAATCATGACATTCTCTAAATAGAAGCTGTCATCGTAGAAACAAGAAGTTAAGTGACTACGGCCTACATGTTGCTTAGCTTCTTTTTTGTG                                                                                                                                       >  2:433908/1‑141
                  AGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGT                                                                                                                                      >  1:73576/1‑141
                           AGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAACTATAAGCTGTCATCGGAAAAAACAGAAATTAAGTGACAACGGCCTCAATGTTTCTTAGCTTCTTTTTTGTGTTGGAAAGct                                                                                                                             >  2:147145/1‑139
                              TGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAA                                                                                                                          >  1:747543/1‑141
                              TGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCCTTTTGGTGTTGGAGAGATGAA                                                                                                                          <  1:405512/141‑1
                                GCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAA                                                                                                                        <  1:498725/141‑1
                                     AATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAG                                                                                                                   <  1:519579/141‑1
                                      aaATTGATAATATTGAAGTGAATATAAAATAATCATGACATTCCTTAAATAGAAGCGGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGC                                                                                                                  <  2:774311/139‑1
                                      ATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGC                                                                                                                  <  1:371094/141‑1
                                         TTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTACATAGAATCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTA                                                                                                               >  1:416087/1‑141
                                           GATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATC                                                                                                             >  1:83441/1‑141
                                           GATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATAGGAAAAACAAGAAGTTAAGTGACAACGGCCTACAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATa                                                                                                             >  2:143705/1‑140
                                                 ATTGAAGTGAATATAGAATCATCATGACATTCTCTAAATAGAAGCTGTAATCGGAAAAACACGAAGTGAAGTGAGAACGGCCTACATGTTACTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCATATCGATGAA                                                                                                       >  1:589322/1‑141
                                                 ATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAA                                                                                                       >  2:664033/1‑141
                                                    GAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAATGGCCTACATGTTGCTTAGCTTCTTTGTTGTGTTGGAGTGATGAAAATGAATCGTATCGATGAATAA                                                                                                    >  2:717450/1‑141
                                                    GAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCTTATCGATGAATAA                                                                                                    >  2:269383/1‑141
                                                    GAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAA                                                                                                    <  1:428021/141‑1
                                                            TATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCGACATGTTGCTTAGCTTCTTCTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACA                                                                                            <  1:418145/141‑1
                                                                AAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGCGAGATGAAAATGAAGCGTCTCGATGAATAATAAAAACACCAA                                                                                        >  2:618916/1‑141
                                                                      TCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAAC                                                                                  <  1:779656/141‑1
                                                                             ATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGA                                                                           >  1:234296/1‑141
                                                                              TTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAA                                                                          >  2:327955/1‑141
                                                                               TCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAA                                                                         <  2:778074/141‑1
                                                                                      ATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTTTTTTTTTTTGATGAAAATGAAGCGTATCGATGATTAATAAAAATACCGATAAAACTTGTGGAAATAGTTGA                                                                  >  2:53523/1‑141
                                                                                          AAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGGTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACT                                                              <  2:255177/141‑1
                                                                                                 CATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTGTGCTTCTCTTCTGTTTAGGAGAGATGAAAATGAAGCATATCGCTGAAGCATAAAAACACCAATAAAACTTGTGGGAATAGTTGATACTTATcatc                                                       >  2:48817/1‑137
                                                                                                    CGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCG                                                    >  2:687022/1‑141
                                                                                                             AAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCT                                           <  2:648011/141‑1
                                                                                                              AGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGTAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAGCTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTT                                          >  1:541829/1‑141
                                                                                                              AGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTT                                          >  1:246997/1‑141
                                                                                                              AGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTT                                          >  1:247036/1‑141
                                                                                                                         GACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAACCTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATG                               <  2:311499/141‑1
                                                                                                                          ACAACGGCCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGA                              <  2:644769/141‑1
                                                                                                                                 CCTACATGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGCAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGAACTGAAACAATG                       >  2:313435/1‑141
                                                                                                                                              TAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGT          <  1:327955/141‑1
                                                                                                                                              TAGCGTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGAGGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGT          <  1:209024/141‑1
                                                                                                                                                GCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTA        >  1:435586/1‑141
                                                                                                                                                 CTTCTTTTTTGAGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATAATTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAA       >  2:625156/1‑141
                                                                                                                                                  TTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAA      >  1:345314/1‑141
                                                                                                                                                     TTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTG   >  1:286322/1‑141
                                                                                                                                                     TTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTG   >  1:286334/1‑141
                                                                                                                                                     TTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTG   >  1:362347/1‑141
                                                                                                                                                     TTTTGTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTG   <  1:487584/141‑1
                                                                                                                                                      TTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACACTGTGGGAAACATAGTTAAATTGA  >  2:396471/1‑141
                                                                                                                                                                                                                                                                                                   
ACAAGAAAATCGCATGGCAGATGTCATAGATGGCACTAATATTGATAACATTGAAGTGAATATAAAATAATCATGACATTCTCTAAATAGAAGCTGTCATCGGAAAAACAAGAAGTTAAGTGACAACGGCCTACATGTTGCTTAGCTTCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/450564‑450716
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTGA  >  USA300TCH1516_ALE/451778‑451915

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