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

AAAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTAA  >  CP000730/2085156‑2085436
                                                                                                                                            |                                                                                                                                            
aaaaaaaGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGtttt                                                                                                                                              >  2:334866/1‑141 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                            <  1:319185‑M1/3‑1 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                            <  2:184800‑M1/3‑1 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtatctaTGt                                                                                                                                            <  1:304834‑M1/3‑1 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactattgttacaaggtgtctaTGt                                                                                                                                            <  1:149958‑M1/3‑1 (MQ=255)
   catccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTa                                                                                                                                           <  1:248249‑M1/4‑1 (MQ=255)
    atccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTAt                                                                                                                                          <  1:267253‑M1/5‑1 (MQ=255)
        ttGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCaa                                                                                                                                      >  1:383446/1‑141 (MQ=255)
        gtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaccccaataaatactgttgttacaaggtgtctaTATATCCaa                                                                                                                                      <  2:200771‑M1/9‑1 (MQ=255)
          tcAACACTTGCATTAGCAAATTTGTTAGTAGTTGGGGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAAc                                                                                                                                    <  2:278759/140‑1 (MQ=255)
          gCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAAc                                                                                                                                    <  2:136608/141‑1 (MQ=255)
             ttctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTgg                                                                                                                                 <  1:141066‑M1/14‑1 (MQ=255)
              cagttGTATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCTAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACCGga                                                                                                                                <  1:286569/138‑1 (MQ=255)
               acTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGgaa                                                                                                                               >  1:105587/1‑140 (MQ=255)
                      ttAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTa                                                                                                                        <  2:327847/141‑1 (MQ=255)
                         gCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACa                                                                                                                     <  1:40618/141‑1 (MQ=255)
                         acAAATTTCTTGTTAGTTGGTGCAATGACTTACAAGAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACa                                                                                                                     <  2:400041/140‑1 (MQ=255)
                             aTTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGACACTTTTAAAATaaa                                                                                                                 >  2:288040/1‑141 (MQ=255)
                              tttATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATaaaa                                                                                                                <  1:37472/141‑1 (MQ=255)
                                tattattaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAAGCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAAtt                                                                                                              <  2:317975/141‑1 (MQ=255)
                                  ttattaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTaa                                                                                                            >  2:334792/1‑140 (MQ=255)
                                     ttaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATATCGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTa                                                                                                         <  2:294783/141‑1 (MQ=255)
                                       aGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTTTATCCAAACTGGAGACTTTTAACATAAAATTACTTATc                                                                                                       <  2:383446/141‑1 (MQ=255)
                                            gaggacaaaaaaaccactcaaattggataaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCa                                                                                                  <  1:293686‑M1/45‑1 (MQ=255)
                                            gaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCa                                                                                                  >  2:248994‑M1/97‑141 (MQ=255)
                                                  ttACTGACAATAGTGTCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGt                                                                                            >  1:306563/1‑141 (MQ=255)
                                                  ttACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGt                                                                                            >  1:237940/1‑141 (MQ=255)
                                                   tgcTGACCATCGTGCCAAGGTCGAATTTAAGAAAGATGATACTGATTTGAATTTAGTTAGTCATAACGTTTATCTGTCATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTa                                                                                           <  2:159927/139‑1 (MQ=255)
                                                   tACTTACAATAGTTCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTa                                                                                           <  2:332647/141‑1 (MQ=255)
                                                   tACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTa                                                                                           >  1:45104/1‑141 (MQ=255)
                                                   aaaaaacaactaaaattttagaaagtatgtaatttagggacctattaggtactccaaacccaataaataatgttggtacacggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTa                                                                                           >  1:393166‑M1/90‑141 (MQ=255)
                                                            aaGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCat                                                                                  <  1:178611/140‑1 (MQ=255)
                                                             aGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCata                                                                                 >  1:358856/1‑141 (MQ=255)
                                                               ggCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataat                                                                               <  2:302643/140‑1 (MQ=255)
                                                                      gCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAGGTAAAACAGCATAATATCAAgg                                                                        >  2:181217/1‑141 (MQ=255)
                                                                       ccGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGt                                                                       >  1:397147/1‑141 (MQ=255)
                                                                       ccGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGt                                                                       >  2:383872/1‑141 (MQ=255)
                                                                              aaagaaagaTGATGATGAATCGAAGTTAGTTAGTCATAACGTTTATATGTCAACGACCGTTTTGTATCCAAACTGGAGACTTTTAACAGTAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAAc                                                                <  1:75555/140‑1 (MQ=255)
                                                                                     gatgatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatca                                                         <  1:10525/141‑1 (MQ=255)
                                                                                           aCTGATTTGCAGTTAGTTAGGCAGAACGTTTAGATGTTATCGACCGTTTTGTATCCAAACGGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATAGCGAGGTTTATAACTttatcattatca                                                   <  2:224698/141‑1 (MQ=255)
                                                                                              gATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaata                                                >  1:10761/1‑141 (MQ=255)
                                                                                                    aaGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGAATTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCt                                          >  2:260139/1‑141 (MQ=255)
                                                                                                     agttagttAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTc                                         >  1:347455/1‑141 (MQ=255)
                                                                                                     agttagttAGTCATAACGTTTATATGTTATAGACCGTTTTGTATCCAAACTGGAGACTTTTAAGATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTc                                         >  2:189928/1‑141 (MQ=255)
                                                                                                     acttagttagTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATAACTTATCACTAAAAAAATAAACAAGAATAATATCAAGGTTTATAACTTTATAATTAACAAAAATACCTc                                         >  2:142663/3‑141 (MQ=255)
                                                                                                        tagttagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGATTTATAACTTTATCATTATCAATAATACCTCata                                      >  2:20758/1‑141 (MQ=255)
                                                                                                                cATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTAATTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATCCCGCATataaaataa                              >  1:111966/1‑141 (MQ=255)
                                                                                                                  caaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATAtaaaataaaa                            >  2:231909‑M1/27‑141 (MQ=255)
                                                                                                                   aaCGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATaaaataaaat                           >  1:24821/1‑141 (MQ=255)
                                                                                                                    aatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTaccactaatacttcacctacaacaacctt                          >  2:233200‑M1/25‑127 (MQ=255)
                                                                                                                    aatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACGTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATAACTAATACCTCATCTTAAATAAAAtt                          >  2:233067‑M1/25‑141 (MQ=255)
                                                                                                                         tataTGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagg                     <  2:10761/141‑1 (MQ=255)
                                                                                                                          atatGTTATCGACCGTATTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGCTTATAACTTTATCATTCTCAATAAAACCTCATATAAAATGAAAttttaggg                    >  1:198579/1‑141 (MQ=255)
                                                                                                                             gttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagtgact                 <  2:212634‑M1/126‑1 (MQ=255)
                                                                                                                                 aTCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTCAAACAACATAATATAAAGGTTTATAACTTTATCATTATAAATAATACCTCATATAAAATAAAAttttagggacttttt             >  2:124445/1‑141 (MQ=255)
                                                                                                                                 aTCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttttt             >  2:124464/1‑141 (MQ=255)
                                                                                                                                          tttGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTttagggactttttagggacttt    >  2:51354/1‑141 (MQ=255)
                                                                                                                                           ttGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACttta   >  2:182920/1‑141 (MQ=255)
                                                                                                                                            TGTATCCGAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCACATATAAAATAAAATTTTAGGGACTCTTTAGAGACtttaa  <  2:227057‑M1/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
AAAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTAA  >  CP000730/2085156‑2085436

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.