New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =15 (0.490)4 (0.150) 4/230 NT 19.3% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 20 (0.730)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128204‑2128482
                                                                                                                                           |                                                                                                                                           
cTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTAAAAGGTTTCTa                                                                                                                                             >  1:216443/1‑140 (MQ=255)
cTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAACAAGGCGGACAAAAAAAGAAATAACATGTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAAACCAATAAATACTGTTGTTACAAGGGTTCTa                                                                                                                                             >  2:163092/1‑140 (MQ=255)
   cATCCGTGTATTCTCATTTGGTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  2:269632‑M2/140‑4 (MQ=255)
      ccGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTAGAAGGTTTCTAtgtatc                                                                                                                                       <  1:297600‑M2/140‑7 (MQ=255)
         tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaa                                                                                                                                    <  1:357613‑M2/140‑10 (MQ=255)
           tATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                  >  1:149427‑M2/1‑129 (MQ=255)
           tATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                  >  2:248277‑M2/1‑129 (MQ=255)
               ctcATCTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTAAGAAAGTATGTAATTTAGGCACCCACTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGATTCTAtgtgtccaacacggg                                                                                                                              <  2:36317‑M2/140‑16 (MQ=255)
                  aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGc                                                                                                                           <  1:331930/140‑1 (MQ=255)
                       ttAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAatat                                                                                                                      >  1:179699/1‑140 (MQ=255)
                           aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                  <  1:340341/140‑1 (MQ=255)
                           aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                  <  2:311541/140‑1 (MQ=255)
                                aaaTTTAATGAAGATGACAAAAAAACAACTAAAATCTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATCCTGTTGTTACAAGTGTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                             <  1:209981/140‑1 (MQ=255)
                                    ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                         >  1:284348/1‑140 (MQ=255)
                                    ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCAATGTATCAAAACTGGGGACAATATAAACGCGCTGAtt                                                                                                         >  1:132416/1‑140 (MQ=255)
                                          aaGAGGACAAAAAAACAACTAAAGTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcat                                                                                                   >  2:102845‑M2/1‑98 (MQ=255)
                                          aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCg                                                                                                   <  1:128925/140‑1 (MQ=255)
                                           agagGACAAAAAAACAACTAAAATTTTTGAAAGTATGTAATTTAGGGACCCTTTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  <  1:319343/140‑1 (MQ=255)
                                           agagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  <  2:48527/140‑1 (MQ=255)
                                               gACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                              <  2:330245/140‑1 (MQ=255)
                                                                      aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAGATAAACGCGCTGAGTGAATCGGACAATCTTCTTATATTAAAAATAatga                                                                       >  1:119170/1‑140 (MQ=255)
                                                                         aaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaacaagtaaaacagcataatatcaagttt                                                                    <  1:151492‑M2/140‑74 (MQ=255)
                                                                            tATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttat                                                                 >  2:207118‑M2/1‑64 (MQ=255)
                                                                                tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAata                                                             <  1:147990/140‑1 (MQ=255)
                                                                                        ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATCATGATGTCGTAATATTTCATGa                                                     >  1:335449/1‑140 (MQ=255)
                                                                                         gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                    >  2:85811/1‑140 (MQ=255)
                                                                                            ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatca                                                 >  1:39191‑M2/1‑48 (MQ=255)
                                                                                                     aCTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAAt                                        >  1:220222/1‑140 (MQ=255)
                                                                                                          aaaCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGc                                   >  1:324509/1‑140 (MQ=255)
                                                                                                            aCCCAAGAAATACTGGTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAACCGCGCTGATTTAATCGGACAATTTTCTTAGATTAAAAATAATGATGTCGTAATATTGAATGAAGCATTTGATAATGGTGCAt                                 <  2:139039/140‑1 (MQ=255)
                                                                                                               cAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAACAg                              >  2:110889/1‑140 (MQ=255)
                                                                                                                  tcaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACa                           <  1:25006/138‑1 (MQ=255)
                                                                                                                  taaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGAAAATGGTGCATCAGACa                           >  1:333407/1‑140 (MQ=255)
                                                                                                                                        gcgaTGTATCCAAAGTGGGGGCAACATAAACGCGCTGATTTAATCGGACAATCGTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaaa     <  2:284348/137‑1 (MQ=255)
                                                                                                                                         cTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTAATAATAGTGCATCAGACAAATTATTAAGTAATGTTaaaaaa    >  2:16983/1‑140 (MQ=255)
                                                                                                                                           aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATAATGAGCTAAAATGCAATGAAGCATTTGATCATGGTGCATCAGACAAATTATTAAGTAATGTGAGAAAAGa  >  1:169471/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                           
CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128204‑2128482

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.