New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	68659 =	76 (0.860)	3 (0.040)	3/242	10.5	4.4%	coding (775/852 nt)	USA300TCH1516_00061	hypothetical protein
	?	USA300TCH1516_ALE	= 68655	63 (0.820)					coding (771/852 nt)	USA300TCH1516_00061	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68800‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523                                                                                                                                                                                                                                                                                     AAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  2:736171/1‑140                                                                                             GGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGA                                             <  1:876471/140‑1                                                                                                     GTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTAATTTTCGACAATATCTATTACAATGTGATTAGAGTGCTTAAGCTCCTTATTGATTTTAAAAGTTTCAGACTTTAAGTAGGAAGGGA                                     >  1:271628/1‑140                                                                                                          CTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTATCGAGGAATGGAAACTT                                >  2:406261/1‑140                                                                                                                             ATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGG             >  1:73717/1‑140                                                                                                                                     TATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGTTTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTT     <  2:209779/140‑1                                                                                                                                     TATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTT     <  2:358191/140‑1                                                                                                                                     TATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTT     <  2:502614/140‑1                                                                                                                                       TTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCC   <  1:102439/140‑1                                                                                                                                       TTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCC   <  1:687570/140‑1                                                                                                                                        TATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGTTTAGAGTGTTTAAGCTCATTATTGATGTAAAAGGTTTCAGAATTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATGTGGAGGTGTTgct  >  2:251569/1‑137                                                                                                                                                                                                                                                                                     AAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68800‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523

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.