New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1443204 =	100 (1.020)	7 (0.110) +CAACGAGCTGTACATTATAAAATACATATC	6/100	NT	10.1%	coding (224/393 nt)	USA300TCH1516_01342	hypothetical protein
	?	USA300TCH1516_ALE	1803072 =	NA (NA)					coding (796/807 nt)	USA300HOU_RS12765	hypothetical protein

TAGTTTTAAACGTGACTTCAAGCTATATGAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1443236‑1443204 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCA  >  USA300TCH1516_ALE/1803072‑1803109                                  ||||||||||||||||||||||||||||||                                       tgGTTTTAAACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTG            <  1:1161468/89‑1   GTTTTAAACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGAT          <  1:3004690/91‑1    TTTTAAACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATA         <  1:588703/91‑1     TTTAAACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAG        <  1:721311/91‑1         AACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT    <  1:1995070/91‑1         AACGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAAT    <  1:3388291/91‑1           CGTGACTTCAAGCTATATGAATGCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCA  <  1:246281/91‑1                                  ||||||||||||||||||||||||||||||                                       TAGTTTTAAACGTGACTTCAAGCTATATGAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1443236‑1443204 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAAAAGCTGATTTCTATTAATTATTTGATAGAAATCA  >  USA300TCH1516_ALE/1803072‑1803109

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