New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1205323	267 (0.930)	25 (0.100) +AGCGAAGCC	10/142	NT	9.6%	intergenic (‑204/‑365)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
	?	USA300TCH1516_ALE	= 1443685	NA (NA)					intergenic (‑258/+95)	USA300TCH1516_01342/brnQ_3	hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein

TACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTATATTA  >  USA300TCH1516_ALE/1443671‑1443775               |                                                                                           tACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCaa                <  1:3704326/91‑1 (MQ=31) tACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCaa                <  1:2817884/91‑1 (MQ=31)  aCGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAAc               >  1:3480044/1‑91 (MQ=32)   cGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAAcc              >  2:1859870/1‑91 (MQ=33)   cGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAAcc              >  1:4274605/1‑91 (MQ=33)    gAAGTATTGTATAAATGGAGAGCAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACct             <  1:3179832/91‑1 (MQ=16)    gAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTTCCAACct             <  1:5424796/91‑1 (MQ=21)    gAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACct             >  1:4886775/1‑91 (MQ=34)    gAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACct             >  1:4365302/1‑91 (MQ=34)    gAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACct             >  1:1572620/1‑91 (MQ=33)    gAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACct             >  2:748531/1‑91 (MQ=34)     aaGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACctc            >  1:1590006/1‑91 (MQ=35)     aaGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACctc            >  1:3917692/1‑91 (MQ=35)      aGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACctct           >  1:2194479/1‑91 (MQ=37)      aGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACctct           <  1:2148849/91‑1 (MQ=37)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGTTTTATGTCCCAACCTCttt         >  2:3154355/1‑91 (MQ=37)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         >  1:1312657/1‑91 (MQ=39)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         >  1:4126258/1‑91 (MQ=39)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         <  2:3413050/91‑1 (MQ=39)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         >  2:1085622/1‑91 (MQ=39)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         <  1:5074551/91‑1 (MQ=39)        tATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCttt         <  1:5377498/91‑1 (MQ=39)         aTTGTATAATTAGAGAGCAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATATCCCAACCTCtttt        >  1:5180612/1‑91 (MQ=255)         aTTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCtttt        >  1:5076019/1‑91 (MQ=37)           tGTATAAATAGAGAACAGCAGTAAGATCTTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtat      >  2:3963507/1‑91 (MQ=37)           tGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtat      <  2:949031/91‑1 (MQ=39)           tGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtat      <  2:1500543/91‑1 (MQ=38)           tGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtat      <  2:3125773/91‑1 (MQ=39)           tGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtat      <  1:1002400/91‑1 (MQ=39)            gTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtata     >  2:121423/1‑91 (MQ=39)            gTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtata     >  1:106774/1‑91 (MQ=38)            gTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtata     >  2:4022378/1‑91 (MQ=39)            gTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTtata     >  1:2640870/1‑91 (MQ=39)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  2:1754597/1‑91 (MQ=39)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  2:882086/1‑91 (MQ=39)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  1:3814212/1‑91 (MQ=39)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  2:2518079/1‑91 (MQ=38)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  2:1910335/1‑91 (MQ=37)             tataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACAGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTatat    >  1:123219/1‑91 (MQ=37)              ataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatt   >  2:2254588/1‑91 (MQ=40)              ataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatt   >  2:2238013/1‑91 (MQ=39)              ataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatt   >  2:3906057/1‑91 (MQ=40)              ataAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatt   >  1:1328789/1‑91 (MQ=40)               taAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatta  <  1:4991264/91‑1 (MQ=255)               taAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatta  >  2:188420/1‑91 (MQ=255)               taAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTAtatta  <  1:4991303/91‑1 (MQ=255)               |                                                                                           TACGAAGTATTGTATAAATAGAGAACAGCAGTAAGATATTTTCTAATTGAAAATTATCTTACTGCTGTTTTTTTAGGGATTTATGTCCCAACCTCTTTTATATTA  >  USA300TCH1516_ALE/1443671‑1443775

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.