New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2031791	102 (1.180)	4 (0.050)	3/286	7.7	4.0%	intergenic (+257/+233)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2031829	96 (1.150)					intergenic (+295/+195)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TCTTTTCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2031639‑2031791 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgactGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAA  <  USA300TCH1516_ALE/2031829‑2031683                                                                                                                                                                                                                                                                                                              TCTTTTCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCCTTGTCTGTAGAAATTGGGAATCCAATTTCTCTATGTTGAGACCCCT                                                                                                                                                         >  1:394956/1‑149    TTTCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCCATTTCTCTTTGTTGGGGCCCCTGAC                                                                                                                                                      >  1:539613/1‑149    TTTCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGAC                                                                                                                                                      >  1:579664/1‑149               TCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCGCAACTTGCATTGTGTGTAGAACTCGGGCATCCACTTTCTGCTTGTTGGCGCCCCTGACTCAACttgcaa                                                                                                                                           >  2:375563/1‑143               TCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTGGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTGAAattgaaa                                                                                                                                           >  1:194883/1‑142                                                  cGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGG                                                                                                        <  2:609426/148‑1                                                     AGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGC                                                                                                     <  1:928779/149‑1                                                                                                                                                    tgtACTGAACGAAAACGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAG      <  1:809240/146‑1                                                                                                                                                     TGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACCAAGAGAAATGGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCACTTTCTACAGA     >  1:444444/1‑149                                                                                                                                                     TGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGA     <  1:864735/149‑1                                                                                                                                                     TGACTGAACGAAAATGCGCTGGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAAAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAAGTGGATACCCAATTTCTACAGA     >  1:135834/1‑149                                                                                                                                                        CTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAA  >  2:716878/1‑149                                                                                                                                                        CTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAA  >  2:717079/1‑149                                                                                                                                                        CTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCACAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAA  >  1:443547/1‑149                                                                                                                                                                                                                                                                                                              TCTTTTCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2031639‑2031791 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgactGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAA  <  USA300TCH1516_ALE/2031829‑2031683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.