New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =19 (0.640)4 (0.150) 4/232 NT 17.4% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 21 (0.790)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432
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aaaaaaGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACAGTTTTg                                                                                                                                         >  1:4320/1‑141 (MQ=255)
 acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                        <  2:181835‑M1/3‑1 (MQ=255)
  catccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTa                                                                                                                                       <  1:233885‑M1/4‑1 (MQ=255)
    tccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATc                                                                                                                                     >  2:316219‑M1/136‑141 (MQ=255)
         gtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                                <  1:19937‑M1/11‑1 (MQ=255)
          cAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACt                                                                                                                               <  1:33031/141‑1 (MQ=255)
              acTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGgag                                                                                                                           <  1:78048/141‑1 (MQ=255)
                 atttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacacactaactactgttgtgacaaggtttctaTGTATCCAAACTGGAGACt                                                                                                                        <  2:162160‑M1/19‑1 (MQ=255)
                         cAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACAt                                                                                                                <  1:334489/141‑1 (MQ=255)
                            aTTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATaaa                                                                                                             <  1:193283/141‑1 (MQ=255)
                              ttattattaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAAt                                                                                                           <  2:250752/141‑1 (MQ=255)
                                   ttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACtt                                                                                                      <  2:353944‑M1/37‑1 (MQ=255)
                                   attaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACtt                                                                                                      >  1:107526/1‑141 (MQ=255)
                                              cACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTCTCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCaaaa                                                                                           >  2:154400/1‑141 (MQ=255)
                                                          aTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCa                                                                               <  2:151396/141‑1 (MQ=255)
                                                                ccAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAatat                                                                         >  1:63435/1‑141 (MQ=255)
                                                                    aGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     >  1:252770/1‑141 (MQ=255)
                                                                    aGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     >  1:252915/1‑141 (MQ=255)
                                                                     gCCGAATCTAAGAAAGATTATACTGATTTGAAGTTAGTCAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAgg                                                                    <  1:242423/141‑1 (MQ=255)
                                                                     gCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAgg                                                                    <  1:305408/141‑1 (MQ=255)
                                                                          gtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTtat                                                               >  1:181835‑M1/66‑141 (MQ=255)
                                                                                  aagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttat                                                       <  1:201668/141‑1 (MQ=255)
                                                                                      tgatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcatt                                                   >  1:280254/1‑141 (MQ=255)
                                                                                        atACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTCTCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattat                                                 >  2:225556/1‑141 (MQ=255)
                                                                                             attagggcctccaaaaccaataactaatgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaata                                            >  1:162160‑M1/47‑141 (MQ=255)
                                                                                                    aatccatacccaataaatcctgttgttacaaggtttctaTGTAGCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTc                                     >  2:341024‑M1/40‑141 (MQ=255)
                                                                                                                      tttATATGTTATCGACCGTTTTGTAACCAAACAGGAGACTTTAACCATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtttta                   <  2:267907/141‑1 (MQ=255)
                                                                                                                           atGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggac              <  1:189338/141‑1 (MQ=255)
                                                                                                                                     ccGTTTTGTCTCCAAACTGAAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATGATACCTCATATAAAATAAAAttttagggactttttagggc    >  1:158851/1‑140 (MQ=255)
                                                                                                                                      cGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagggac   >  2:317989/1‑141 (MQ=255)
                                                                                                                                       ttgttGTATCCAAACTGGACACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTGTATCATTATCAATAATCCCTCATATAAAATAAAAtgttagggactttttagggact  <  1:53010/138‑1 (MQ=255)
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AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.