New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1353906	40 (1.430)	3 (0.120)	3/252	3.5	8.2%	intergenic (+99/+44)	nucH/USA300HOU_RS06735	Thermonuclease/hypothetical protein
	?	USA300TCH1516_ALE	= 1353932	31 (1.230)					intergenic (+125/+18)	nucH/USA300HOU_RS06735	Thermonuclease/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGCACAAAATAAAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1353759‑1353906 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggcataataaTCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACTTTAATATATATAATCACCTATTTAATTATTTACTCCA  <  USA300TCH1516_ALE/1353932‑1353796                                                                                                                                                                                                                                                                                               AGCATAAAAGAAAGGTAAATTACAGAAATTTTATTTTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGG                                                                                                                                                   <  2:131414/140‑1        AATAAAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATc                                                                                                                                            >  1:110325/1‑139        AATAAAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                                                                            <  1:210117/140‑1        AATAAAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                                                                            >  2:210070/1‑140                                               TAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTT                                                                                                     <  1:232655/140‑1                                                                           AGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGG                                                                         >  2:12178/1‑140                                                                                                             CCATAAATTTATATATATAAATAATTTAAAGGCATAATAATCCATTCTGTTCGATACACACCATCGTTATCATCTTTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACT                                       <  1:12178/140‑1                                                                                                                                        AAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTGCAAGTATATTTTACTTTAATATATATAATCACCTATTTAATa            >  1:280001/1‑139                                                                                                                                                  TAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACTTTAATATATATAATCACCTATTTAATTATTTACTCCA  <  2:293093/140‑1                                                                                                                                                  TAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACTTTAATATATATAATCACATATTTAAATATTTACTCCA  >  2:113639/1‑140                                                                                                                                                  TAATCCAGTACGCGCGATACGCACTAGGGGTATTATGCCTTTAAATTATTGCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACTTTAATATATATAATCACCTATTTAATTATTTACTCCA  <  1:204455/140‑1                                                                                                                                                                                                                                                                                               AGCACAAAATAAAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1353759‑1353906 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggcataataaTCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGTATATTTTACTTTAATATATATAATCACCTATTTAATTATTTACTCCA  <  USA300TCH1516_ALE/1353932‑1353796

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.