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

ACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTAAATTTAAAATTAC  >  CP000730/2085171‑2085448
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acTTGCATTAGCAAATTTNTTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGga                                                                                                                                            <  1:306851/140‑1 (MQ=255)
   tGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATATTACCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGAc                                                                                                                                         <  1:280539/140‑1 (MQ=255)
       gtaccaaatTTATTAGTAGTTGGTGTGCTTACTGACACTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGgggcaata                                                                                                                                     <  2:81047‑M1/136‑9 (MQ=255)
              aTTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATaa                                                                                                                              >  1:175144/1‑140 (MQ=255)
                         gTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATc                                                                                                                   <  1:238607/140‑1 (MQ=255)
                           aagaggacaaaaaaacaactaaagttttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCAt                                                                                                                 >  2:102845‑M1/99‑140 (MQ=255)
                             gTGCACTTAGTGACAATAGAGCCAAACCTGAATCTACGAAACATGACACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCATTTTGTATCCAAACTGGAGACTTTTAACATAAAATTAATTATCATTc                                                                                                               >  2:67586/1‑140 (MQ=255)
                                  cTTACTGACAATAGTGACAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggacaatc                                                                                                          <  2:44665‑M1/140‑36 (MQ=255)
                                   ttagggACAATCGTGCCAAAGGCTAATCTAAGAAAGATGAGACTGATGTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAg                                                                                                         <  1:45989/135‑1 (MQ=255)
                                      cTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGATTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCACAAACTaa                                                                                                      >  2:293594/1‑140 (MQ=255)
                                            aTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGATAGTTAGTCATAACGTTTATATGTGATCGACCGTTTTGTATACAAACTGGgggcaatataaacgcgctgatttaatcggaaaaactacttgtatt                                                                                                >  2:34939‑M1/1‑95 (MQ=255)
                                                        ccGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAga                                                                                    >  2:75944/1‑139 (MQ=255)
                                                          aagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAACAAGTAAAACAGCATAATATcaagttt                                                                                  <  1:151492‑M1/73‑4 (MQ=255)
                                                             tatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTtat                                                                               >  2:207118‑M1/65‑140 (MQ=255)
                                                                aagaaagaTGATACTGAGCTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTGTTATCATCGCATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAAc                                                                            <  1:50614/140‑1 (MQ=255)
                                                                aagaaagaTGATACAGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGTATAATATCAAGGCTTATAAc                                                                            <  1:222921/140‑1 (MQ=255)
                                                                      gatgatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatc                                                                      <  2:354666/140‑1 (MQ=255)
                                                                         gatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCACACTGGgggcaatataaacgcgcggatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatga                                                                   >  2:310326‑M1/1‑66 (MQ=255)
                                                                             cggatTTGTAGTTAGTTAGTCATAACGTTTATATTTTATCGACCGTGTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatgaagca                                                               <  1:118490‑M1/138‑79 (MQ=255)
                                                                             ccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                                               >  1:39191‑M1/49‑140 (MQ=255)
                                                                             cTGATTTGAAGTTAGATAGTCATATAGTTTATCTGTTATCGACCGTTTTGAATCCAAACTGGAGACTTTTAACATAAAATTACTTATTATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                                               <  1:206556/140‑1 (MQ=255)
                                                                                      ttgtatttagtTATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACCGCATAATATCAAGGTTTATAACTGTATCATTATCAATAATACCt                                                      <  1:216339/134‑1 (MQ=255)
                                                                                                      cGTTTATATGTTATCTACCCTTTTGTATCCAAACTAGAGACTTTTAACATAAAATTACTTATCATTCCAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtt                                      <  2:215222/140‑1 (MQ=255)
                                                                                                                   tCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttttt                         <  2:175144/140‑1 (MQ=255)
                                                                                                                       ccGTTTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggaccatgttcgaaaattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattattaagtaatgtgaaa                     <  1:350536‑M1/140‑121 (MQ=255)
                                                                                                                               tATCCAAACTGGgggcaatataaacgcgctgatttaatcggacaatcttcttatattaaacataatgatgtcgtaatattcaatgaagcatttgataatggtgcataagacaaattaataattaatgtgaaaaaagaata             >  1:298356‑M1/1‑12 (MQ=255)
                                                                                                                               TATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACtttaaa             <  1:199491‑M1/140‑1 (MQ=255)
                                                                                                                                  CCAAACTGGAGACTTTTAACATAAAATTACTTATCATTTAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACtttaaattt          >  1:333196‑M1/1‑140 (MQ=255)
                                                                                                                                   cAAACTGGgggcaatataaacgcgctaatttaatcggacaaactacttatattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattattaagtaatgtgaaaaaagaatatcct         <  1:67993‑M1/140‑133 (MQ=255)
                                                                                                                                     aaCTGGgggcaatataaacgcgctgatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattcttaagtaatgtgaaaaaagaatatcctta       >  2:329639‑M1/1‑6 (MQ=255)
                                                                                                                                         gggggcaatataaacgcgctgatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattattaagtaatgtgaaaaaagaatatccttatcaa   <  1:16990‑M1/140‑139 (MQ=255)
                                                                                                                                          ggggcaatataaacgcgctgatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattattaagtaatgtgaaaaaagaatatccttatcaaa  >  1:233364‑M1/1‑1 (MQ=255)
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ACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTAAATTTAAAATTAC  >  CP000730/2085171‑2085448

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.