New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =31 (1.170)29 (1.220) 25/230 NT 58.8% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 13 (0.550)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128204‑2128481
                                                                                                                                           |                                                                                                                                          
cTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATCCTGTTGTTACAAGGTTTCTa                                                                                                                                            >  1:61254/1‑140 (MQ=255)
  aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtg                                                                                                                                          <  2:142183‑M2/140‑3 (MQ=255)
   cagccttgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGt                                                                                                                                         <  2:111362/134‑1 (MQ=255)
   cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAAACCAATAAATACGATTGTTACAAGGTTACAAtgt                                                                                                                                         <  1:249814‑M2/140‑4 (MQ=255)
        gtgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcca                                                                                                                                    <  1:147565‑M2/140‑9 (MQ=255)
         tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaa                                                                                                                                   <  2:204187‑M2/140‑10 (MQ=255)
         tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTGTCTAtgtatccaa                                                                                                                                   <  2:286414‑M2/140‑10 (MQ=255)
            aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaact                                                                                                                                >  1:183187‑M2/1‑128 (MQ=255)
             ttCACATTTGTGAAAAGAAAAATTTAAAGAAGAAGACAAAAAAACAACTAAAAATTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactg                                                                                                                               >  1:275482‑M2/1‑127 (MQ=255)
                  aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagac                                                                                                                          >  2:250922‑M2/1‑122 (MQ=255)
                      gTTAAAAGAAAAATTAAATGACGAAGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAACTTATGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagactttt                                                                                                                      >  2:111568‑M2/1‑118 (MQ=255)
                          gaagaaAAATTTAATGAAGCGTACAAAAAAACATTTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaaca                                                                                                                  >  1:6677‑M2/1‑114 (MQ=255)
                          aaagaaAAATCTAAACAAAAGGACAAAAAAACAACTAAAATTTTATAAAGTATGTAATTTATGGACCCATTAGGGACTCCAAACCCAATAAATACGGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATaaa                                                                                                                  <  2:115880/139‑1 (MQ=255)
                           aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacat                                                                                                                 >  1:207934‑M2/1‑113 (MQ=255)
                                aaaTTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                            <  2:12746/140‑1 (MQ=255)
                                 aaaTTAATGAAGAGGACAAAAAAACAACCAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaatt                                                                                                           >  2:3917‑M2/1‑107 (MQ=255)
                                  aTTTAATGAAGAGAACAAAAAAACAACAAAAAATTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAACACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaatta                                                                                                          >  1:80930‑M2/1‑106 (MQ=255)
                                   tttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAt                                                                                                         <  1:253058/140‑1 (MQ=255)
                                     tAATGAAGAAGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTCGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattactt                                                                                                       >  2:217971‑M2/1‑103 (MQ=255)
                                       aTGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttat                                                                                                     <  1:58727‑M2/140‑40 (MQ=255)
                                        tGAAGGGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatc                                                                                                    >  1:272249‑M2/1‑100 (MQ=255)
                                         gAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATc                                                                                                   <  2:250507/140‑1 (MQ=255)
                                          aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCCTGAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTTTAtgtatccaaactggagacttttaacataaaattacttatcat                                                                                                  >  2:175299‑M2/1‑98 (MQ=255)
                                              ggACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaacttaattatcattcaa                                                                                              <  1:38460‑M2/140‑47 (MQ=255)
                                              ggACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaa                                                                                              <  1:136063‑M2/140‑47 (MQ=255)
                                                aCAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaa                                                                                            >  2:296805‑M2/1‑92 (MQ=255)
                                                     aaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAAtcttct                                                                                       <  1:308606/140‑1 (MQ=255)
                                                       aacaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaa                                                                                     >  1:89671‑M2/1‑85 (MQ=255)
                                                       aacaacTAAAAGTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaa                                                                                     >  1:37152‑M2/1‑85 (MQ=255)
                                                           acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagc                                                                                 <  1:99280‑M2/140‑60 (MQ=255)
                                                           acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagc                                                                                 <  1:99284‑M2/140‑60 (MQ=255)
                                                                    tgaGAAAGTATGTAATTTAGGGCCCCATTAGGGAGTCCCAACCCAATACATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAGATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaataat                                                                        <  2:99372/138‑1 (MQ=255)
                                                                            tATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttat                                                                >  2:305533‑M2/1‑64 (MQ=255)
                                                                              tGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataa                                                              >  2:61254‑M2/1‑62 (MQ=255)
                                                                                    ttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttat                                                        >  1:263563‑M2/1‑56 (MQ=255)
                                                                                           cccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGc                                                 >  1:272023/1‑140 (MQ=255)
                                                                                            ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                                <  2:266940/140‑1 (MQ=255)
                                                                                               ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaata                                             <  2:189158‑M2/140‑96 (MQ=255)
                                                                                               ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaata                                             >  1:41251‑M2/1‑45 (MQ=255)
                                                                                                tAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattataaataa                                            <  2:166336‑M2/140‑97 (MQ=255)
                                                                                                   ggACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTCAAAATAATGATGTCGTAATATTCAATGCAGAATTTGATa                                         >  2:290930/1‑140 (MQ=255)
                                                                                                         cAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTg                                   <  1:163454/140‑1 (MQ=255)
                                                                                                           aaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaacgtaaaacagcataatatcaaggtttataaatttatactaaacaataatacctcatatc                                 <  2:262794‑M2/140‑108 (MQ=255)
                                                                                                           aaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatata                                 <  1:56065‑M2/140‑108 (MQ=255)
                                                                                                                 ataaataCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataa                           <  1:112276‑M2/140‑114 (MQ=255)
                                                                                                                   aaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGATTTTTATAATGGTGCATCAGACaa                         <  2:147565/140‑1 (MQ=255)
                                                                                                                     ataCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaatt                       <  1:63082‑M2/140‑118 (MQ=255)
                                                                                                                      taCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGAATTTGATAATGGTGCATCAGACAAatt                      >  1:128841/1‑140 (MQ=255)
                                                                                                                        cTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGATGATTTAATGGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTAAATGAAGAATTTGATAATGGTGCATAAGACAAagtat                    >  2:92220/1‑140 (MQ=255)
                                                                                                                            tgttACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttaggga                >  1:200866‑M2/1‑16 (MQ=255)
                                                                                                                                aCAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggacttt            >  1:277909‑M2/1‑12 (MQ=255)
                                                                                                                                 cAAGGTTTCTAtgtaaccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttt           <  1:236916‑M2/140‑130 (MQ=255)
                                                                                                                                       ttCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttaggga     <  1:69148‑M2/140‑136 (MQ=255)
                                                                                                                                          tAtgtatccaaactggatacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattataaataataccaaatatataataaaattttaggctctttttagggtctt  <  2:127756‑M2/140‑139 (MQ=255)
                                                                                                                                          tAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttagggactt  <  1:146104‑M2/140‑139 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128204‑2128481

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.