New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 557256NA (NA)33 (0.130) 13/142 NT NA intergenic (+314/‑1455) USA300TCH1516_00504/USA300TCH1516_00505 tRNA‑Ala/tRNA‑Ile
?USA300TCH1516_ALE = 557260 NA (NA)intergenic (+318/‑1451) USA300TCH1516_00504/USA300TCH1516_00505 tRNA‑Ala/tRNA‑Ile

GGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATA  >  USA300TCH1516_ALE/557174‑557297
                                                                                  |                                         
ggagAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGAGAACATTTTGAACCGCATGGtt                                   >  2:495810/4‑91 (MQ=0)
                                 cttggAGAACTTCGGGAATCCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTtata  <  1:4735633/88‑1 (MQ=0)
                                                                                  |                                         
GGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATA  >  USA300TCH1516_ALE/557174‑557297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ 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.