New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2713224	51 (1.100)	3 (0.070)	3/242	NT	5.6%	intergenic (‑322/+286)	isaA/USA300HOU_RS13945	putative transglycosylase IsaA/hypothetical protein
	?	USA300TCH1516_ALE	= 2713244	53 (1.230)					intergenic (‑342/+266)	isaA/USA300HOU_RS13945	putative transglycosylase IsaA/hypothetical protein

TGTTATTTGTAATGTTGAAATATGGCTGTTTTATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2713077‑2713224 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atattacagCTATGTAACAAAAATACAATCTGTAATATTACGAAAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTATGTGTTAAAGACTATTTCAAGGGTTGATTGGATTCTAAAGGGCACATATTTCACATTACAGTATAAAA  <  USA300TCH1516_ALE/2713244‑2713105                                                                                                                                                                                                                                                                                                  ttTNANTTGTAATGTTCAAATATAGCTTTTTTATACTGTAATATGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAATCTTTAACACATAAGATTNTTANTATATTTNGCTCAACTATTACAGCTTTCGTAAT                                                                                                                                                     <  1:36809/139‑1       TTGTAATGTTGAAATATGGCTGTTTTATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACA                                                                                                                                               >  2:308407/1‑141                                   ACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGCTATGTAACAAAAATACAATCTGTAAT                                                                                                                   <  1:562104/141‑1                                                                                AAATAGTCTTTAACACATTAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGCTATGTAACAAAAATACAATCTGTAATATTACGAAAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTA                                                                      <  1:261190/141‑1                                                                                                   AGATTTTTACTATATTTAGCTCATCTATTACAGCTTTCGTAATATTACAGCTATGTAACAAAAATACAATCTGTAATATTACGATAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTATGTGTTAAAGACTATTTCA                                                   <  1:226234/141‑1                                                                                                                                                TACAGCTATGTAACAAAAATACAATCTGTAATATTACGAAAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTATGTGTTAAAGACTATTTCAAGGGTTGATTGGATTCTAAAGGGCACATATTTCACATTACAGTAT      <  1:168443/141‑1                                                                                                                                                    GCTATGTAACAAAAATACAATCTGTAATATTACGAAAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTATGTGTTAAAGACTATTTCAAGGGTTGATTGGATTCTAAAGGGCACATATTTCACATTACAGTATAAAA  >  1:361692/1‑141                                                                                                                                                                                                                                                                                                  TGTTATTTGTAATGTTGAAATATGGCTGTTTTATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2713077‑2713224 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atattacagCTATGTAACAAAAATACAATCTGTAATATTACGAAAGCTGTAATAGTTGAGCTAAATATAGTAAAAATCTTATGTGTTAAAGACTATTTCAAGGGTTGATTGGATTCTAAAGGGCACATATTTCACATTACAGTATAAAA  <  USA300TCH1516_ALE/2713244‑2713105

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.