New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 801934	87 (0.980)	5 (0.060) +C	3/256	NT	5.5%	intergenic (+175/+449)	USA300HOU_0748/dgkA1	hypothetical protein/possible diacylglycerol kinase
	?	CP000730	= 2145702	86 (0.970)					intergenic (+236/‑125)	USA300HOU_2028/orf5	possible nitroreductase/amidohydrolase

GTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/801868‑801934 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGGCCCCAACATAGAGAAATTGGAACACCAATTTCTACAGACAATGCAAGTTGGGGTGGGCTCTAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAT  <  CP000730/2145702‑2145595                                                                    |                                                                                                             GTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAA                                     <  1:183755/141‑1 GTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAA                                     <  2:369948/141‑1    GTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTGGGAGGGGGC‑CCAACATAAAGGAA                                 >  2:1028140/1‑141                                    gcgttCCAATTTCTACAGACAATGCAAGTTGGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAT  <  1:245553/136‑1                                    gcgttCCAATTTCTACAGACAATGCAAGTTGGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAT  >  2:245553/6‑141                                                                    |                                                                                                             GTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/801868‑801934 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGGCCCCAACATAGAGAAATTGGAACACCAATTTCTACAGACAATGCAAGTTGGGGTGGGCTCTAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAT  <  CP000730/2145702‑2145595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.