New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 1526	45 (0.790)	4 (0.010) +TTG	4/250	7.7	1.4%	intergenic (+311/‑545)	repA/USA300HOU_pUSA300HOUMR0003	replication protein A/hypothetical protein
	?	NC_012417	= 997	548 (0.910)					intergenic (+9/+6)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000731/1463‑1526 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTCTTCTTCGTCTGTTGTTTTATCTTCATCACTTGCATTAATCAAATTACCATCTTCGACAT  <  NC_012417/997‑872                                                                 |||                                                                                                                               AAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCT                                                                  >  2:182518/1‑129             TTACCGCAATTTTGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTCTTCTTCG                                                      <  2:159133/129‑1                              TTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTCTTCTTCGTCTGTTGTTTTATCTTC                                     <  2:147650/129‑1                                               TTATTTAAGAAATTAGTGTTGGCTAATGTCTTCAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTGTTCTTCGTCTGTTGTTTTATCTTCATCACTTGCATTAATCA                    >  1:162346/1‑129                                                                 TTGACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTCTTCTTCGTCTGTTGTTTTATCTTCATCACTTGCATTAATCAAATTACCATCTTCGACAT  >  2:131014/1‑129                                                                 |||                                                                                                                               AAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000731/1463‑1526 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ACTAATGTCTTAAATAATAATTTTGCTTTTCGAAATTCCAAATTGCGGTAATTGAATGTGCTTTTTCTTCTTCGTCTGTTGTTTTATCTTCATCACTTGCATTAATCAAATTACCATCTTCGACAT  <  NC_012417/997‑872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.