New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 208530913 (0.420)6 (0.220) 6/230 NT 27.5% intergenic (‑571/‑387) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 2128358 = 20 (0.730)intergenic (+72/+1047) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

ATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCAAA  >  CP000730/2128222‑2128496
                                                                                                                                        |                                                                                                                                          
aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGc                                                                                                                                         <  1:331930/140‑1 (MQ=255)
    gtaccaaatttattagtagttggtgtgcttactgacactagtgccaaagccgaatctaagaaagatgatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccaaactggGGGCAata                                                                                                                                     <  2:81047‑M2/8‑1 (MQ=255)
     ttAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAatat                                                                                                                                    >  1:179699/1‑140 (MQ=255)
         aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                                <  2:311541/140‑1 (MQ=255)
         aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                                <  1:340341/140‑1 (MQ=255)
              aaaTTTAATGAAGATGACAAAAAAACAACTAAAATCTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATCCTGTTGTTACAAGTGTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                                           <  1:209981/140‑1 (MQ=255)
                  ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                                       >  1:284348/1‑140 (MQ=255)
                  ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCAATGTATCAAAACTGGGGACAATATAAACGCGCTGAtt                                                                                                                       >  1:132416/1‑140 (MQ=255)
                        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)
                               cttactgacaatagtgacaaagccgaatctaagaaagatgatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAAtc                                                                                                          <  2:44665‑M2/35‑1 (MQ=255)
                                         atagtgccaaagccgaatctaagaaagatgatactgatttgaagatagttagtcataacgtttatatgtgatcgaccgttttgtatacaaactggGGGCAATATAAACGCGCTGATTTAATCGGAAAAACTACTTGTAtt                                                                                                >  2:34939‑M2/96‑140 (MQ=255)
                                                    aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAGATAAACGCGCTGAGTGAATCGGACAATCTTCTTATATTAAAAATAatga                                                                                     >  1:119170/1‑140 (MQ=255)
                                                              tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAata                                                                           <  1:147990/140‑1 (MQ=255)
                                                                      ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATCATGATGTCGTAATATTTCATGa                                                                   >  1:335449/1‑140 (MQ=255)
                                                                      gatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccacactggGGGCAATATAAACGCGCGGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGa                                                                   >  2:310326‑M2/67‑140 (MQ=255)
                                                                       gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                                  >  2:85811/1‑140 (MQ=255)
                                                                          cggatttgtagttagttagtcataacgtttatattttatcgaccgtgttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                                               <  1:118490‑M2/78‑1 (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)
                                                                                                                    ccgttttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACCATGTTCGAAAATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaa                     <  1:350536‑M2/120‑1 (MQ=255)
                                                                                                                      gcgaTGTATCCAAAGTGGGGGCAACATAAACGCGCTGATTTAATCGGACAATCGTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaaa                   <  2:284348/137‑1 (MQ=255)
                                                                                                                       cTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTAATAATAGTGCATCAGACAAATTATTAAGTAATGTTaaaaaa                  >  2:16983/1‑140 (MQ=255)
                                                                                                                         aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATAATGAGCTAAAATGCAATGAAGCATTTGATCATGGTGCATCAGACAAATTATTAAGTAATGTGAGAAAAGa                >  1:169471/1‑140 (MQ=255)
                                                                                                                            tatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAACATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATAAGACAAATTAATAATTAATGTGAAAAAAGAata             >  1:298356‑M2/13‑140 (MQ=255)
                                                                                                                                caaactggGGGCAATATAAACGCGCTAATTTAATCGGACAAACTACTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCt         <  1:67993‑M2/132‑1 (MQ=255)
                                                                                                                                  aactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTCTTAAGTAATGTGAAAAAAGAATATCCTTa       >  2:329639‑M2/7‑140 (MQ=255)
                                                                                                                                      ggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCaa   <  1:16990‑M2/138‑1 (MQ=255)
                                                                                                                                       gGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCaaa  >  1:233364‑M2/2‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                          
ATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCAAA  >  CP000730/2128222‑2128496

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.