New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =40 (1.200)7 (0.240) 6/232 NT 17.6% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 30 (1.010)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085445‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  CP000730/2128343‑2128206
                                                                                                                                                                                                                                                                                                
ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATAAAAAATTGTTTATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTACAGT                                                                                                                                                     <  1:272056/141‑1
   TTAAATTTAAAGTCCCTACAAAATTCCTAAAATCTTATTTTATATGAGGTAGTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTG                                                                                                                                                  >  2:283208/1‑141
   TTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATCTGATGTTGTATGGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATCAGTAATTTTATGTTTAAAGTCGTCAGTTTG                                                                                                                                                  >  1:310937/1‑141
    TAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGG                                                                                                                                                 <  1:171508/141‑1
     AAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGA                                                                                                                                                <  1:236218/141‑1
         TTAAAGTCTCTAAAGAGTCCCTAAAATTTTATTTTATATGTGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTCGGATACA                                                                                                                                            <  2:227057/141‑1
                        AGTCACTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAAC                                                                                                                             <  2:212634/141‑1
                                 aaggttgttgtaggTGAAGTATTAGTGGTAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATT                                                                                                                    >  2:233200/15‑141
                                 AATTTTATTTAAGATGAGGTATTAGTTATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATACGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATT                                                                                                                    >  2:233067/1‑141
                                   TTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTg                                                                                                                  >  2:231909/1‑140
                                                                                                  TACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCGTGTACCAACATTATTTATTGGGTTTGGAGTACCTAATAGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTT                                                   >  1:393166/1‑141
                                                                                                         TGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTC                                            >  2:248994/1‑141
                                                                                                         TGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTATCCAATTTGAGTGGTTTTTTTGTCCTC                                            <  1:293686/141‑1
                                                                                                                                        CCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAA             <  1:141066/141‑1
                                                                                                                                             TTGGATATATAGACACCTTGTAACAACAGTATTTATTGGGGTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACAC        <  2:200771/141‑1
                                                                                                                                                 ATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGAT    <  1:267253/141‑1
                                                                                                                                                  TACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATG   <  1:248249/141‑1
                                                                                                                                                   ACATAGATACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  1:304834/141‑1
                                                                                                                                                   ACATAGACACCTTGTAACAATAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  1:149958/141‑1
                                                                                                                                                   ACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  2:184800/141‑1
                                                                                                                                                   ACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  1:319185/141‑1
                                                                                                                                                                                                                                                                                                
ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085445‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT  <  CP000730/2128343‑2128206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.