New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =40 (1.200)7 (0.240) 6/232 NT 17.6% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 30 (1.010)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128206‑2128482
                                                                                                                                         |                                                                                                                                           
aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  1:319185‑M2/141‑4 (MQ=255)
aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  2:184800‑M2/141‑4 (MQ=255)
aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTATCTAtgt                                                                                                                                          <  1:304834‑M2/141‑4 (MQ=255)
aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTATTGTTACAAGGTGTCTAtgt                                                                                                                                          <  1:149958‑M2/141‑4 (MQ=255)
 cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgta                                                                                                                                         <  1:248249‑M2/141‑5 (MQ=255)
  aTCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtat                                                                                                                                        <  1:267253‑M2/141‑6 (MQ=255)
      gtgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGTGTCTAtatatccaa                                                                                                                                    <  2:200771‑M2/141‑10 (MQ=255)
           ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                               <  1:141066‑M2/141‑15 (MQ=255)
              tcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACTAGGTTTCTATGTATCCAAACTggggg                                                                                                                            <  2:247474/141‑1 (MQ=255)
                   tGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAata                                                                                                                       <  1:20966/141‑1 (MQ=255)
                         aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcg                                                                                                                 <  2:66168/141‑1 (MQ=255)
                           gaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcgcg                                                                                                               <  2:186329/141‑1 (MQ=255)
                                 tttAATGAAGAGGACAAAAAAACAACTATCATTATAGAAATGATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                         <  1:171200/141‑1 (MQ=255)
                                  ttAATGAAGAGGACAAAAAAACAACTACAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACGGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAttt                                                                                                        <  1:34517/141‑1 (MQ=255)
                                        aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  >  1:44943/1‑141 (MQ=255)
                                          gagGACAAAAAAACCACTCAAATTGGATAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattca                                                                                                <  1:293686‑M2/141‑46 (MQ=255)
                                          gagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattca                                                                                                >  2:248994‑M2/1‑96 (MQ=255)
                                                 aaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCTATTAGGTACTCCAAACCCAATAAATAATGTTGGTACACGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagta                                                                                         >  1:393166‑M2/1‑89 (MQ=255)
                                                  aaaaaCAACTAAAATGTTAGAAAGTATGTAATGTAGGGACCCATTAGGGACTCCAAGCCCAATAAATACTGTTGTTACAAGGCTTCTATGTATCCAAACTGGGGGTAATATAAACTCGCTGATTTGATCGGACAAtcttct                                                                                        <  1:200771/141‑1 (MQ=255)
                                                    aaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTta                                                                                      <  2:341638/141‑1 (MQ=255)
                                                      acaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTtata                                                                                    >  1:3012/1‑141 (MQ=255)
                                                      acaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTtata                                                                                    <  2:211638/141‑1 (MQ=255)
                                                        aacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATAtt                                                                                  >  2:53917/1‑141 (MQ=255)
                                                        aacTAAAAATTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTTACCAAACTGGGGGCCATATAAACGCGCTGATTTAATCGGACAATCTTCTTATAtt                                                                                  >  2:294162/1‑141 (MQ=255)
                                                         acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCGAAAATGGGCGCTATATATACGCGCTGAGTTCATCGGCCAATCTCGTTATATTa                                                                                 >  1:350890/1‑141 (MQ=255)
                                                         acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAACCTTCTTACATTa                                                                                 >  2:79944/1‑141 (MQ=255)
                                                         acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTGATGGGAGAATATTGTTATAGTa                                                                                 >  1:61543/1‑141 (MQ=255)
                                                                     gAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatgatg                                                                     <  2:44943/141‑1 (MQ=255)
                                                                       aaGTATGTAATGTAGGAACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAGGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTc                                                                   <  1:311771/141‑1 (MQ=255)
                                                                         gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGt                                                                 <  1:326651/141‑1 (MQ=255)
                                                                               aaTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTCACAAGGTTTCTATGTATCCAAACTGGGGGCCATATAAACGCGCTGATTTAATCGGACAATCTTGTTATATTAAAAATAATTATGTCGTaaaagt                                                           >  2:253968/1‑137 (MQ=255)
                                                                                     gggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGa                                                     >  2:371381/1‑141 (MQ=255)
                                                                                             ttAGGGACTCCAAACCCAGTAAATACTGTTGTTACAAGGTTTCTATGTATCCACACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGACGTAATATTCAATGAAGCATTTg                                             >  2:61154/1‑141 (MQ=255)
                                                                                               aGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGAt                                           >  1:116463/1‑141 (MQ=255)
                                                                                                    cTCCAAACCCAATAAATCCGGTCGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:288641/141‑1 (MQ=255)
                                                                                                    cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATTATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:191938/141‑1 (MQ=255)
                                                                                                    cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:117643/141‑1 (MQ=255)
                                                                                                       cAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGc                                   <  2:248249/141‑1 (MQ=255)
                                                                                                                caaatacTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaa                          >  2:231909‑M2/2‑26 (MQ=255)
                                                                                                                  aataCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattaccactaatacttcacctacaacaacctt                        >  2:233200‑M2/1‑24 (MQ=255)
                                                                                                                  aataCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacgtatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattataactaatacctcatcttaaataaaatt                        >  2:233067‑M2/1‑24 (MQ=255)
                                                                                                                  aataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAat                        <  2:304834/141‑1 (MQ=255)
                                                                                                                          tgttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGt                <  1:122206/141‑1 (MQ=255)
                                                                                                                           gttACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagtgact               <  2:212634‑M2/141‑127 (MQ=255)
                                                                                                                             tACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACCAATTATTAAGTAAt             >  2:52187/1‑141 (MQ=255)
                                                                                                                             tACAAGGTTTCTACGTATCAAAACTGGGGGCAATATAAACGCGCTAATTTAAAAAGAAAAAAAACTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGAATTTGATAATGGTGCATCAGATAACTTATTaaaaaat             <  2:350890/141‑6 (MQ=255)
                                                                                                                                        tATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGa  >  1:150997/1‑141 (MQ=255)
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ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128206‑2128482

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.