New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	66 (0.940)	5 (0.080)	5/232	NT	8.0%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	56 (0.900)					intergenic (+57/+1062)	int/USA300HOU_2011	bacteriophage integrase/possible leukocidin subunit

TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085449‑2085296 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  <  CP000730/2128343‑2128205                                                                                                                                                                                                                                                                                                       TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATCTTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTC                                                                                                                                                          >  2:570820/1‑141  GTAATTTTAAATTTAAGGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGTTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAATTCTCC                                                                                                                                                         <  2:417281/141‑1   TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCA                                                                                                                                                        >  1:92662/1‑141   TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCA                                                                                                                                                        >  1:578355/1‑141   TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCA                                                                                                                                                        >  1:704020/1‑141   TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCA                                                                                                                                                        >  2:676923/1‑141   TAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTATCCA                                                                                                                                                        >  2:339075/1‑141     ATTTTAAATTGAAAGTCACCAATAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                      <  1:262537/141‑1      TTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTT                                                                                                                                                     >  2:831514/1‑141        taAAATTTAAAGGCCCTAAAAAGTCCCTAAAAATTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTG                                                                                                                                                   <  1:328110/139‑1         TAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTGGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGG                                                                                                                                                  >  2:8137/1‑141          AAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGA                                                                                                                                                 >  1:518035/1‑141           AATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGTTTGTTTTTTAATTTTATGTTAAAAGTCTCCAGTTTGGtt                                                                                                                                                >  2:292449/1‑139                                                               TGATAATGATAAAGTTATAAACCTTGATATTCTGCTGTTTTACTTTTTGAATGATCAGTAATTTTATGTTAAAGGTCTCCAGTTTGGGTAGATAGAAACCTTGTAACAACAGTCTTTCTTGGGTTTGGAGTCCCTAATGGG                                                                                            >  1:30764/1‑141                                                                   AATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCC                                                                                        <  2:551256/141‑1                                                                             TTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACAT                                                                              >  2:309021/1‑141                                                                                                                       AGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGTAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAA                                    <  2:366021/141‑1                                                                                                                         TAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTGTTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATT                                  >  1:740833/1‑141                                                                                                                                          TCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGA                 <  2:112820/141‑1                                                                                                                                                 TTTGGATACCTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA          <  2:451821/141‑1                                                                                                                                                 TTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA          <  1:174858/141‑1                                                                                                                                                   TGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACG        <  1:811339/141‑1                                                                                                                                                   TGGATACATAGAAACCTTGTAACAACAGTACTTATTGGGTTTGGAGTCCCTCATGGGTACCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTTCTCTTCATTAAATTTTTATTCTTACAAATGAGAATACACG        >  2:43024/1‑141                                                                                                                                                   TGGATAAACAGAAACCTTGTAACAACAGTATTTTTTGGGTTTGGAGTCCCTAATGGGTCACCAAATTAACTACTTTATAAAATTTTAGTTGTTTTTTTGTCCTCTGCATTAAATTTTTCTTCTAACAAATGAGAATACACG        <  1:801729/141‑1                                                                                                                                                        atATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGT   <  2:269818/139‑1                                                                                                                                                         CATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  >  1:772641/1‑141                                                                                                                                                                                                                                                                                                       TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085449‑2085296 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTA  <  CP000730/2128343‑2128205

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.