New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =26 (0.820)30 (1.060) 21/232 NT 56.5% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 23 (0.810)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

TACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAA  >  CP000730/2128205‑2128478
                                                                                                                                          |                                                                                                                                        
tACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACACAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtg                                                                                                                                        <  1:253415‑M2/141‑3 (MQ=255)
 aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGAATCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                       <  1:132945‑M2/141‑4 (MQ=255)
 aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGAGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAAGATTCTAtgt                                                                                                                                       <  2:118388‑M2/141‑4 (MQ=255)
   aTCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGAACCATTAGGGACTCCAAACACAATAAATACTGTTGTTACAAGGTTTCTAtgtat                                                                                                                                     <  1:55647‑M2/141‑6 (MQ=255)
     ccGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcc                                                                                                                                   <  1:323772‑M2/141‑8 (MQ=255)
         gtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                               >  1:144900‑M2/1‑130 (MQ=255)
         gtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                               >  1:343572‑M2/1‑130 (MQ=255)
             tctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACACATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgga                                                                                                                           <  2:227578‑M2/141‑16 (MQ=255)
                cATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactcgagac                                                                                                                        <  2:278184‑M2/141‑19 (MQ=255)
                      ttAGAAGAAAAACTTAAAGAAAAAGACAAAAAAATAACTAAATTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAtata                                                                                                                  <  1:143118/141‑1 (MQ=255)
                           agaaAAATTGAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcgc                                                                                                             <  1:79022/141‑1 (MQ=255)
                            gaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTGTGTAATTTAGGGACCCATTAGGGACTCCAAAACCAATAAATGCTATTGTTACAAGGTTTCTGtgtatgcaaactggagacttttaacataaa                                                                                                            <  1:43537‑M2/141‑31 (MQ=255)
                              aaaaTTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaat                                                                                                          >  1:23905‑M2/1‑109 (MQ=255)
                                    tAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattactta                                                                                                    >  1:212445‑M2/1‑103 (MQ=255)
                                       tGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatca                                                                                                 <  1:291245‑M2/141‑42 (MQ=255)
                                       tGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatca                                                                                                 >  2:4191‑M2/1‑100 (MQ=255)
                                        gAAGAGGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcat                                                                                                >  2:188943‑M2/1‑99 (MQ=255)
                                                   aaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAAGCGCTGATTTAATCGGACAAtcttct                                                                                    >  1:117507/1‑141 (MQ=255)
                                                     aaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGAAATATAATCTCGCCGCTTTAATTGGACAATCTTCTta                                                                                  >  2:173077/1‑141 (MQ=255)
                                                          acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTa                                                                             >  1:36592/1‑141 (MQ=255)
                                                               aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataata                                                                         >  1:319080‑M2/1‑76 (MQ=255)
                                                                aTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaata                                                                       <  2:2733/141‑1 (MQ=255)
                                                                  tttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatca                                                                      <  2:47814‑M2/141‑69 (MQ=255)
                                                                   ttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatg                                                                    <  1:19367/141‑1 (MQ=255)
                                                                      aaaagTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacaacataatatcaaggt                                                                  >  1:250133‑M2/2‑69 (MQ=255)
                                                                         aGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggttta                                                               >  2:339181‑M2/1‑66 (MQ=255)
                                                                         aGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggttta                                                               >  2:214512‑M2/1‑66 (MQ=255)
                                                                              gTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAata                                                         >  2:33521/1‑141 (MQ=255)
                                                                                aaTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATAtt                                                       >  2:359449/1‑141 (MQ=255)
                                                                                   ttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatc                                                     <  1:366282‑M2/141‑86 (MQ=255)
                                                                                   ttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatc                                                     <  2:37674‑M2/141‑86 (MQ=255)
                                                                                   ttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcaaaatatcaaggtttataactttata                                                     <  2:307894‑M2/141‑86 (MQ=255)
                                                                                       ggACCCATTAGGGACTCCAAACCCAATCAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattccaaaagtaaaacagcataatatcaaggtttataactttatcattt                                                 <  1:129519‑M2/141‑90 (MQ=255)
                                                                                       ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattgaaaaagtaagacagcataatatcaaggtttataactttatcatta                                                 <  1:259427‑M2/141‑90 (MQ=255)
                                                                                       ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGAGTTCTAGGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATACTGAAGTCGTAATATAAAATGaa                                                >  2:81029/1‑141 (MQ=255)
                                                                                        gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAg                                               >  1:136744/1‑141 (MQ=255)
                                                                                        gACCCATTAGGGACTCCAAACCCAATAAAAACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAg                                               <  2:211957/141‑1 (MQ=255)
                                                                                        gACCCATTAGGGACCCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTACGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATTTTAAGAATAATGATGTCGTAATATTCAATGAAg                                               <  2:253052/141‑1 (MQ=255)
                                                                                         aCCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatc                                               <  1:152272‑M2/141‑92 (MQ=255)
                                                                                         aCCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGATTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatc                                               <  1:148751‑M2/141‑92 (MQ=255)
                                                                                           ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttataactatcaa                                             <  2:339538‑M2/141‑94 (MQ=255)
                                                                                           ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCAt                                            >  1:321561/1‑141 (MQ=255)
                                                                                            cATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaat                                            >  2:13503‑M2/1‑47 (MQ=255)
                                                                                            cATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattaccaat                                            >  2:265020‑M2/1‑47 (MQ=255)
                                                                                              ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataa                                          <  1:17253‑M2/141‑97 (MQ=255)
                                                                                               tAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggcgacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataat                                         <  2:300874‑M2/141‑98 (MQ=255)
                                                                                               tAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataat                                         <  1:6769‑M2/141‑98 (MQ=255)
                                                                                                  ggACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATaa                                     <  1:186935/141‑1 (MQ=255)
                                                                                                  ggAATCCAAAACCAATAAATACTGTTGATACAAGGTTTCTAGGTATCCAAACTGGGGACAATATAAACGCGCTGATTTAATCAGACAAACATCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATaa                                     <  1:14015/141‑1 (MQ=255)
                                                                                                        cAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGc                               <  1:71642/141‑1 (MQ=255)
                                                                                                         aaaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatata                               <  1:62574‑M2/141‑108 (MQ=255)
                                                                                                          aaCCGAATCAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAt                             <  1:316886/141‑1 (MQ=255)
                                                                                                          aaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtagtgatactggagcattggaacttaaaattacttatcattcaaaaagtaaaacagcataatatcaagatttataactttatcattatcaataatacctcatataa                              <  1:90066‑M2/141‑109 (MQ=255)
                                                                                                          aaCCCAATAAAAACTGTTGATACAAGGTTTCTAtgtatccaaactggagacttttaacaaaaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataa                              <  2:120386‑M2/141‑109 (MQ=255)
                                                                                                           aCCCAATAAATACTGTTGTTACAAGGTGTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATc                            <  1:831/141‑1 (MQ=255)
                                                                                                                atatataCTGTTGTTACCAGGTTTCTTTGTAACCAAAATGAAAGTATATAACGACAGCTGATATAACCTGACAACCTTCTTATATTAAAAATAATGTTGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACa                       <  2:269497/141‑1 (MQ=255)
                                                                                                                      aCTGTTTCTACAAGGTTTACATGTATGGAAATTGGGTGGAACATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTTGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAattat                 <  1:173077/141‑1 (MQ=255)
                                                                                                                      aCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaatttta                  <  1:277060‑M2/141‑121 (MQ=255)
                                                                                                                      aCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacatcatataaaataaaatttta                  <  1:300805‑M2/141‑121 (MQ=255)
                                                                                                                            gttACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggact            <  2:116063‑M2/141‑127 (MQ=255)
                                                                                                                               aCAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGACGCCCGTCAAAAGGAAGCATGTGATAATGGTGCATCAGACAAATTATTAAGTAAtg        >  1:180179/1‑141 (MQ=255)
                                                                                                                                cAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAGTGGTGCATCAGACAAATTATTAAGTAAtgt       >  1:119000/1‑141 (MQ=255)
                                                                                                                                      ttCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttagggac  <  2:26421‑M2/141‑137 (MQ=255)
                                                                                                                                          |                                                                                                                                        
TACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAA  >  CP000730/2128205‑2128478

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