New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1470058	85 (0.980)	4 (0.050)	3/286	7.7	4.4%	intergenic (‑105/‑240)	USA300TCH1516_01369/rnhA	hypothetical protein/14.7 kDa ribonuclease H‑like protein
	?	USA300TCH1516_ALE	= 2031786	93 (1.110)					intergenic (+252/+238)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CATTATTGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1469908‑1470058 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcaGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGAGAATTTCGAAAAGA  <  USA300TCH1516_ALE/2031786‑2031639                                                                                                                                                                                                                                                                                                             CATTATTGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGT                                                                                                                                                        <  2:858149/149‑1   TTATTGTACGCTGACAGTTCGTCATCTTCGGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCA                                                                                                                                                      >  2:544343/1‑149   TTATTGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGGATTTGGGTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAGAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCA                                                                                                                                                      >  2:232660/1‑149   TTATTGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAACGCTTGTTACAAGCGCATTTTCGTTCAGTCA                                                                                                                                                      >  2:652992/1‑149       TGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCCGTCtactc                                                                                                                                                  >  2:404813/1‑144                                                                                                   GCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCT                                                      >  1:928779/1‑149                                                                                                      CCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACg                                                   >  2:609426/1‑148                                                                                                                                         tttcaatTTCAGTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCCACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGA                <  1:194883/142‑1                                                                                                                                         ttgcaaGTTGAGTCAGGGGCGCCAACAAGCAGAAAGTGGATGCCCGAGTTCTACACACAATGCAAGTTGCGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGA                <  2:375563/143‑1                                                                                                                                                    GTCAGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGAGAATTTCGAAA     <  1:579664/149‑1                                                                                                                                                    GTCAGGGGCCCCAACAAAGAGAAATGGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGAGAATTTCGAAA     <  1:539613/149‑1                                                                                                                                                       AGGGGTCTCAACATAGAGAAATTGGATTCCCAATTTCTACAGACAAGGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGAGAATTTCGAAAAGA  <  1:394956/149‑1                                                                                                                                                                                                                                                                                                             CATTATTGTAAGCTGACTTTTCGTCATCTTCTGTGTTGGGACCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1469908‑1470058 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agtcaGGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACAAAGAGAAATTGGATTCCCAATTTCTACAGACAATGCAAGTTGGGGTGTGGGCCCCAACACAGAGAATTTCGAAAAGA  <  USA300TCH1516_ALE/2031786‑2031639

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.