New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2144160	31 (0.870)	4 (0.120) +TGGTTTATCT	3/260	3.3	12.2%	coding (484/1254 nt)	USA300HOU_RS10940	hypothetical protein
	?	USA300TCH1516_ALE	2144165 =	31 (0.870)					coding (479/1254 nt)	USA300HOU_RS10940	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TCTGGTGACGGGTTAGGATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2144063‑2144160 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGG  >  USA300TCH1516_ALE/2144165‑2144235                                                                                                   ||||||||||                                                                        TCTGGTGACGGGTTAGGATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGTTTTGGTTTCGGG                                        >  2:28879/1‑141                 gagtgGGCTTATTAGGGTCTGGTTTTGGAGTCGGATTTGGCTGTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGTTTTGGTTTCGGGTTATCTGGATCTGGTT                        <  2:121483/136‑1                 GATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGTTTTGGTTTCGGGTTATCTGGATCTGGTT                        <  1:203225/141‑1                                       TTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTTGGATCCAGATTTGGCTTTGG  <  1:28879/141‑1                                                                                                   ||||||||||                                                                        TCTGGTGACGGGTTAGGATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2144063‑2144160 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGG  >  USA300TCH1516_ALE/2144165‑2144235

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.