Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EA87_1-HE.fastq.uq.polyn	EA87_1-HE.filter	percent
uq reads:	49613272	2407200	4.8519%
   reads: 	54567997	2577952	4.7243%
----------------
virus_structural_rna_repbase_filter:
  reads:	EA87_1-HE.filter	EA87_1-HE.nostrna	percent
uq reads:	2407200	2271914	94.3799%
   reads: 	2577952	2399977	93.0963%
----------------
TE_filter:
  reads:	EA87_1-HE.nostrna	EA87_1-HE.noTE	percent
uq reads:	2271914	2265599	99.7220%
   reads: 	2399977	2390338	99.5984%
----------------
match_dm6_mask_gen:1:
  reads:	EA87_1-HE.noGEN.front	EA87_1-HE.noGEN.front.gen	percent
uq reads:	2265599	1277641	56.3931%
   reads: 	2390338	1316342	55.0693%
----------------
match_TE:2:
  reads:	EA87_1-HE.noGEN.front	EA87_1-HE.noGEN.front.TE	percent
uq reads:	2265599	146525	6.4674%
   reads: 	2390338	153469	6.4204%
----------------
match_dm6_mask_gen:1:
  reads:	EA87_1-HE.noGEN.end	EA87_1-HE.noGEN.end.gen	percent
uq reads:	2265599	1236959	54.5974%
   reads: 	2390338	1277870	53.4598%
----------------
match_TE:2:
  reads:	EA87_1-HE.noGEN.end	EA87_1-HE.noGEN.end.TE	percent
uq reads:	2265599	144824	6.3923%
   reads: 	2390338	151906	6.3550%
----------------
Candidate insertion sites in file: EA87_1-HE_insert.txt
  reads:	34679
  uqreads:	32794
  Number of Candidate sites:	32794

Level 1 collapse of insertion sites in file: EA87_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	656

Level 1 annotation file: EA87_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EA87_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EA87_1-HE.noGEN.front	EA87_1-HE.noGEN.front.gendel	percent
uq reads:	2265599	1277641	56.3931%
   reads: 	2390338	1316342	55.0693%
----------------
match_dm6_mask_gen_del:1:
  reads:	EA87_1-HE.noGEN.end	EA87_1-HE.noGEN.end.gendel	percent
uq reads:	2265599	1236959	54.5974%
   reads: 	2390338	1277870	53.4598%
----------------
Candidate breakpoint sites in file: EA87_1-HE_depletion.xls
  reads:	120051
  uqreads:	114460
  Number of reads supporting candidate sites:	114460

Level 1 collapse of depletion sites in file: EA87_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	4273