New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2635582	50 (1.400)	4 (0.110) +TCT	3/274	3.5	7.7%	coding (366/3057 nt)	fnbA_2	Fibronectin‑binding protein A
	?	USA300TCH1516_ALE	2635601 =	48 (1.340)					coding (347/3057 nt)	fnbA_2	Fibronectin‑binding protein A
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTGTAGCCTTTTTAGGTGTTAAATCTACTTGTCTTTGATCTCCGCTATTGTCTTGAGATTGTGTTGTTTCCTTAACTTGAGGTTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2635497‑2635582 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCTTCTTTAACTGTTTCTATATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTACTGCTTTTGGTGCTTCTTCAGTTGT  >  USA300TCH1516_ALE/2635601‑2635677                                                                                       |||                                                                              GTGTAACCTTTTTAGGTGTTAAATCTACTTGTCTTTGATTTCCGCTATTGTCTTGAGGTTGTGTCGTTTCCTTAACTTGAGGTTTCTCTTCTTCTTTAACTGTTTCTACATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTA                           >  1:76418/1‑141 GTGTAACCTTTTTAGGTGTTAAATCTACTTGTCTTTGATTTCCGCTATTGTCTTGAGGTTGTGTCGTTTCCTTAACTTGAGGTTTCTCTTCTTCTTTAACTGTTTCTACATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTA                           >  2:139872/1‑141                        TCTACTTGTCTTTGATTTCCGCTATTGTCTTGAGGTTGTGTCGTTTCCTTAACTTGAGGTTTCTCTTCTTCTTTAACTGTTTCTACATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTACTGCTTTTGGTGCTTCTTCAGTT    <  1:12592/141‑1                          TACTTGTCTTTGATTTCCGCTATTGTCTTGAGGTTGTGTCGTTTCCTTAACTTGAGGTTTCTCTTCTTCTTTAACTGTTTCTACATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTACTGCTTTTGGTGCTTCTTCAGTTGT  <  2:385960/141‑1                                                                                       |||                                                                              GTGTAGCCTTTTTAGGTGTTAAATCTACTTGTCTTTGATCTCCGCTATTGTCTTGAGATTGTGTTGTTTCCTTAACTTGAGGTTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2635497‑2635582 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCTTCTTTAACTGTTTCTATATTTGCTGGTTGTGCAGTTTGTGGTGCTTGTACTGCTTTTGGTGCTTCTTCAGTTGT  >  USA300TCH1516_ALE/2635601‑2635677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.