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

TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085447‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  CP000730/2128343‑2128206
                                                                                                                                                                                                                                                                                                  
TAATTTTAAATTTAAAGTCTCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                        <  1:175300/140‑1
TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                        <  1:95056/140‑1
TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                        <  2:304011/140‑1
 AATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATACGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTATCCA                                                                                                                                                       <  2:194245/140‑1
  ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAG                                                                                                                                                      <  2:13401/140‑1
  ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGAATTATTGATAATGATAAAGTTATAAACCTTGATATTTTGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAG                                                                                                                                                      >  2:97863/1‑140
  ATTTTAAATTTAAAATCCCGAAAAATTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAG                                                                                                                                                      >  1:176067/1‑140
   TTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                     >  2:99284/1‑140
   TTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                     >  2:203030/1‑140
   TTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                     >  2:99280/1‑140
        AATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGA                                                                                                                                                >  2:237046/1‑140
              AAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATA                                                                                                                                          <  1:146104/140‑1
              AAGACCCTAAAAAGAGCCTAAAATTTTATTATATATTTGGTATTATTTATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTATCCAGTTTGGATACATA                                                                                                                                          <  2:127756/140‑1
                 TCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAA                                                                                                                                       <  1:69148/140‑1
                       AAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGTTACATAGAAACCTTG                                                                                                                                 <  1:236916/140‑1
                        AAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGT                                                                                                                                >  1:277909/1‑140
                            TCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACA                                                                                                                            >  1:200866/1‑140
                                   AATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTAT                                                                                                                     <  1:63082/140‑1
                                       TTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTAT                                                                                                                 <  1:112276/140‑1
                                             gATATGAGGTATTATTGTTTAGTATAAATTTATAAACCTTGATATTATGCTGTTTTACGTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTT                                                                                                           <  2:262794/139‑1
                                             TATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTT                                                                                                           <  1:56065/140‑1
                                                        TTATTTATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTA                                                                                                <  2:166336/140‑1
                                                         TATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAA                                                                                               <  2:189158/140‑1
                                                         TATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAA                                                                                               >  1:41251/1‑140
                                                                    ATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAA                                                                                    >  1:263563/1‑140
                                                                          TTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACA                                                                              >  2:61254/1‑140
                                                                            ATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATA                                                                            >  2:305533/1‑140
                                                                                             GCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGT                                                           <  1:99280/140‑1
                                                                                             GCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGT                                                           <  1:99284/140‑1
                                                                                                 TTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAACTTTTAGTTGTT                                                       >  1:37152/1‑140
                                                                                                 TTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTT                                                       >  1:89671/1‑140
                                                                                                        TTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGT                                                >  2:296805/1‑140
                                                                                                          TTGAATGATAATTAAGTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCC                                              <  1:38460/140‑1
                                                                                                          TTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCC                                              <  1:136063/140‑1
                                                                                                              ATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAAAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTCAGGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTT                                          >  2:175299/1‑140
                                                                                                                GATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCCCTTCA                                        >  1:272249/1‑140
                                                                                                                 ATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCAT                                       <  1:58727/140‑1
                                                                                                                   AAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCGAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTTTCTTCTTCATTA                                     >  2:217971/1‑140
                                                                                                                      TAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTGTTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAATTTTTTGTTGTTTTTTTGTTCTCTTCATTAAAT                                  >  1:80930/1‑140
                                                                                                                       AATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTGGTTGTTTTTTTGTCCTCTTCATTAATTT                                 >  2:3917/1‑140
                                                                                                                             ATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTT                           >  1:207934/1‑140
                                                                                                                              TGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAAATGTTTTTTTGTACGCTTCATTAAATTTTTCTTC                          >  1:6677/1‑140
                                                                                                                                  AAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCATAAGTTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCTTCGTCATTTAATTTTTCTTTTAAC                      >  2:111568/1‑140
                                                                                                                                      GTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAAT                  >  2:250922/1‑140
                                                                                                                                           CAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAATTTTTAGTTGTTTTTTTGTCTTCTTCTTTAAATTTTTCTTTTCACAAATGTGAA             >  1:275482/1‑140
                                                                                                                                            AGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAAT            >  1:183187/1‑140
                                                                                                                                               TTGGATACATAGACACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA         <  2:286414/140‑1
                                                                                                                                               TTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA         <  2:204187/140‑1
                                                                                                                                                TGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACAC        <  1:147565/140‑1
                                                                                                                                                     ACATTGTAACCTTGTAACAATCGTATTTATTGGTTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATG   <  1:249814/140‑1
                                                                                                                                                      CATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  2:142183/140‑1
                                                                                                                                                                                                                                                                                                  
TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085447‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  CP000730/2128343‑2128206

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.