New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =50 (0.650)19 (0.280) 14/232 NT 25.9% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 64 (0.940)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085448‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  <  CP000730/2128343‑2128205
                                                                                                                                                                                                                                                                                                    
GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                         >  1:17037/1‑141
GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                         >  1:684986/1‑141
   ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                      <  1:148316/141‑1
      TTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATACTGCTAAAGTTATAAATCTGGATGTTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTG                                                                                                                                                   >  1:261838/1‑141
      TTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTG                                                                                                                                                   >  1:520774/1‑141
        AAATTTAAAGTCCCTAAAAAGTCATTCCAGCTTTAGGTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGA                                                                                                                                                 >  1:669914/1‑141
         AATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGAT                                                                                                                                                <  1:635267/141‑1
          ATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGAAAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATA                                                                                                                                               >  1:606528/1‑141
           TTTAAATTCCCTAAAAAGCCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATAC                                                                                                                                              <  1:716805/141‑1
             TAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACAT                                                                                                                                            >  2:894915/1‑141
             TAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTAATTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTACAGTTTGGATAaca                                                                                                                                            >  2:124472/1‑138
                 GTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTAGATATTATGCTGTTTTACTCTTAGAATGATAAGTAATTATCGGAAAAAAGTCTCAAGTTTGGATACATAGAA                                                                                                                                        >  2:829045/1‑141
                     CTAAAAAGTTCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCT                                                                                                                                    <  2:563654/141‑1
                                      TTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTA                                                                                                                   <  2:669914/141‑1
                                         TATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTTTTTTTTTTTTAATTTTATGTTGAAAGTCTCCAGTTTTGATACATAGAAATCTTGTAACAACATTATTTTTTG                                                                                                                >  2:403199/1‑141
                                             TTATATGAGGTATTATTTATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTT                                                                                                            <  2:202021/141‑1
                                             TTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTT                                                                                                            <  1:313327/141‑1
                                                         TTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAA                                                                                                >  1:29479/1‑141
                                                            TTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGATGGATAAGTATTTTTCTGAGAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGG                                                                                             >  1:435794/1‑141
                                                            TTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGG                                                                                             >  2:790044/1‑141
                                                                                AACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTCAATTACATACTTT                                                                         >  1:876167/1‑141
                                                                                AACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTT                                                                         >  2:779173/1‑141
                                                                                AACCTTGATATTATCCTGTGTTACTATTTGAATGATAAGTAATTATATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAAGGGGTCCCTAAATTACATACTTT                                                                         >  1:499180/1‑141
                                                                                     TGATATTAAGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAA                                                                    <  1:454777/141‑1
                                                                                       ATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAAT                                                                  >  1:483199/1‑141
                                                                                             TGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGT                                                            <  1:890694/141‑1
                                                                                             TGCTGTTTTACCTTTTGAAGGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGT                                                            <  1:801024/141‑1
                                                                                                 GTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTCGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTT                                                        <  2:327748/141‑1
                                                                                                                 GATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCAT                                        <  1:578754/141‑1
                                                                                                                     atTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAA                                    <  1:288475/139‑1
                                                                                                                         ATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTCTTTTTGTCCTCTTCATTAAATTTT                                <  1:664869/141‑1
                                                                                                                                          TCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGA               >  1:760396/1‑141
                                                                                                                                            CAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAAT             <  2:360403/141‑1
                                                                                                                                             AGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATA            <  1:878085/141‑1
                                                                                                                                             AGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCATCTTCATTAAATTTTTCTTCTAACAAATGAGAATA            >  1:47812/1‑141
                                                                                                                                               TTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTGGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA          <  1:144167/141‑1
                                                                                                                                                TTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAACTTTTTCTTCTAACAAATAAGAATACAC         >  2:334620/1‑141
                                                                                                                                                   GATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCGTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGA      <  1:518982/141‑1
                                                                                                                                                    ATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTTGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAAGATACACTGAT     >  1:509825/1‑141
                                                                                                                                                    ATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGAT     >  1:284423/1‑141
                                                                                                                                                     TACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATG    <  1:502050/141‑1
                                                                                                                                                      ACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT   >  2:105472/1‑141
                                                                                                                                                       CATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  <  2:520774/141‑1
                                                                                                                                                                                                                                                                                                    
GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085448‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  <  CP000730/2128343‑2128205

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.