New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =38 (1.060)15 (0.460) 8/252 1.7 35.2% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 21 (0.650)intergenic (+57/+1062) int/hlgB bacteriophage integrase/possible leukocidin subunit

AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432
                                                                                                                                           |                                                                                                                                        
tacatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTg                                                                                                                                         >  1:269560‑M1/140‑141 (MQ=255)
    tccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATc                                                                                                                                     >  1:63505‑M1/136‑141 (MQ=255)
    tccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATc                                                                                                                                     >  2:362549‑M1/136‑141 (MQ=255)
     ccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaattatgtattttagggacccattaggtactccaaacccaataaatactgttgttacaagggttctaTGTATcc                                                                                                                                    <  1:329175‑M1/7‑1 (MQ=255)
     ccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATcc                                                                                                                                    <  1:86152‑M1/7‑1 (MQ=255)
     ccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATcc                                                                                                                                    <  1:66249‑M1/7‑1 (MQ=255)
     ccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATcc                                                                                                                                    <  1:79941‑M1/7‑1 (MQ=255)
         gtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                                <  1:229465‑M1/11‑1 (MQ=255)
         gtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                                <  1:213687‑M1/11‑1 (MQ=255)
           aaCACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATATTGCCAAATCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTg                                                                                                                              <  2:140610/141‑1 (MQ=255)
              ctcatttgttagaagaaaaatttaatgcagaggacaaaaaaacaactaaaattgtagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTggaa                                                                                                                           <  2:113057‑M1/16‑2 (MQ=255)
              ctcatttgtgagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGgag                                                                                                                           <  2:144530‑M1/16‑1 (MQ=255)
                   aaTTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACttt                                                                                                                      >  2:4091/2‑141 (MQ=255)
                   aaTTAGCAAATTTATTATTAGTGGGTGCACTTACTGACAATAGTGCCAACGCCGAATCTAAGAAAGATGATACTGATTTGAAGTCAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGCGACttt                                                                                                                      >  2:4012/2‑141 (MQ=255)
                                                    aaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTaaa                                                                                     >  1:279695‑M1/88‑141 (MQ=255)
                                                    aaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTaaa                                                                                     >  1:53540‑M1/88‑141 (MQ=255)
                                                        caactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAg                                                                                 >  2:211626‑M1/84‑141 (MQ=255)
                                                        caactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAg                                                                                 >  2:379952‑M1/84‑141 (MQ=255)
                                                        caactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAg                                                                                 >  2:166745‑M1/84‑141 (MQ=255)
                                                             gTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataa                                                                            >  1:245884/1‑141 (MQ=255)
                                                             gTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataa                                                                            >  1:360703/1‑141 (MQ=255)
                                                             gTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataa                                                                            >  1:396162/1‑141 (MQ=255)
                                                             gTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGCCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAGAGTAAAACAGCataa                                                                            >  2:309780/1‑141 (MQ=255)
                                                                   aaGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCaa                                                                      <  1:63139/141‑1 (MQ=255)
                                                                   aaGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCaa                                                                      <  2:341130/141‑1 (MQ=255)
                                                                   aaGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATAATTCAAAAAGTAAAACAGCATAATATCaa                                                                      <  2:331819/141‑1 (MQ=255)
                                                                   aaGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTAATCGACCGTTTTGTATCCAAACTGGCGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCaa                                                                      <  1:41120/141‑1 (MQ=255)
                                                                    tagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     <  2:149720‑M1/70‑1 (MQ=255)
                                                                    tagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     <  1:345104‑M1/70‑1 (MQ=255)
                                                                         agtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTta                                                                >  1:211455‑M1/67‑141 (MQ=255)
                                                                               agaaagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                          <  2:221415/141‑1 (MQ=255)
                                                                               agaaagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                          <  2:317934/141‑1 (MQ=255)
                                                                               agaaagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                          <  2:92265/141‑1 (MQ=255)
                                                                               agaaagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                          >  1:367225/1‑141 (MQ=255)
                                                                               agaaagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                          <  1:409283/141‑1 (MQ=255)
                                                                                       ggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcatta                                                  <  2:11307‑M1/89‑1 (MQ=255)
                                                                                       ggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcatta                                                  <  1:96916‑M1/89‑1 (MQ=255)
                                                                                        atACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattat                                                 >  2:146272/1‑141 (MQ=255)
                                                                                        atACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattat                                                 >  2:125933/1‑141 (MQ=255)
                                                                                        atACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattat                                                 >  2:108567/1‑141 (MQ=255)
                                                                                         tACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCACACTGGAGCCTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatc                                                <  1:186122/141‑1 (MQ=255)
                                                                                         tACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatc                                                <  1:680/141‑1 (MQ=255)
                                                                                          aCTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                               >  1:20767/1‑141 (MQ=255)
                                                                                          aCTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                               >  1:318690/1‑141 (MQ=255)
                                                                                            cattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaat                                             <  1:141865‑M1/94‑1 (MQ=255)
                                                                                                          aacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataa                               <  2:14571‑M1/108‑1 (MQ=255)
                                                                                                          aacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTAGCATTATCAATAATACCTCATataa                               <  2:122136‑M1/108‑1 (MQ=255)
                                                                                                           tagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATAAATCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataaa                              <  2:286045/141‑1 (MQ=255)
                                                                                                           tagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTAATTATCAATCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataaa                              <  2:60048/141‑1 (MQ=255)
                                                                                                                aTAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataaaataaa                         <  1:310348/141‑1 (MQ=255)
                                                                                                                      tttATATGTTATCGACCGTTTTTTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATGCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtttta                   <  1:83474/141‑1 (MQ=255)
                                                                                                                      tttATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCGTTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtttta                   <  2:252239/141‑1 (MQ=255)
                                                                                                                         atatGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttaggg                >  1:65723/1‑141 (MQ=255)
                                                                                                                           atGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggac              >  2:74079/1‑141 (MQ=255)
                                                                                                                               tATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttt          <  2:360703/141‑1 (MQ=255)
                                                                                                                               tATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttt          <  2:245884/141‑1 (MQ=255)
                                                                                                                               tATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttt          <  2:396162/141‑1 (MQ=255)
                                                                                                                                   gACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagg      <  2:318690/141‑1 (MQ=255)
                                                                                                                                   gACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagg      <  2:20767/141‑1 (MQ=255)
                                                                                                                                       gTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCGTTATCAATAATACGGCATAGAACATAAGAttttagggactttttagggact  >  1:120366/1‑141 (MQ=255)
                                                                                                                                       gTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagggact  >  2:91586/1‑141 (MQ=255)
                                                                                                                                       gTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttttnagggact  >  2:310705/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                        
AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432

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