Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EB25_1-HE.fastq.uq.polyn	EB25_1-HE.filter	percent
uq reads:	25816877	2143908	8.3043%
   reads: 	30771620	2878489	9.3544%
----------------
virus_structural_rna_repbase_filter:
  reads:	EB25_1-HE.filter	EB25_1-HE.nostrna	percent
uq reads:	2143908	1143758	53.3492%
   reads: 	2878489	1232697	42.8244%
----------------
TE_filter:
  reads:	EB25_1-HE.nostrna	EB25_1-HE.noTE	percent
uq reads:	1143758	1136166	99.3362%
   reads: 	1232697	1221807	99.1166%
----------------
match_dm6_mask_gen:1:
  reads:	EB25_1-HE.noGEN.front	EB25_1-HE.noGEN.front.gen	percent
uq reads:	1136166	566758	49.8834%
   reads: 	1221807	595485	48.7381%
----------------
match_TE:2:
  reads:	EB25_1-HE.noGEN.front	EB25_1-HE.noGEN.front.TE	percent
uq reads:	1136166	117194	10.3149%
   reads: 	1221807	127731	10.4543%
----------------
match_dm6_mask_gen:1:
  reads:	EB25_1-HE.noGEN.end	EB25_1-HE.noGEN.end.gen	percent
uq reads:	1136166	542264	47.7275%
   reads: 	1221807	572927	46.8918%
----------------
match_TE:2:
  reads:	EB25_1-HE.noGEN.end	EB25_1-HE.noGEN.end.TE	percent
uq reads:	1136166	113344	9.9760%
   reads: 	1221807	123928	10.1430%
----------------
Candidate insertion sites in file: EB25_1-HE_insert.txt
  reads:	20199
  uqreads:	17991
  Number of Candidate sites:	17991

Level 1 collapse of insertion sites in file: EB25_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	546

Level 1 annotation file: EB25_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EB25_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EB25_1-HE.noGEN.front	EB25_1-HE.noGEN.front.gendel	percent
uq reads:	1136166	566758	49.8834%
   reads: 	1221807	595485	48.7381%
----------------
match_dm6_mask_gen_del:1:
  reads:	EB25_1-HE.noGEN.end	EB25_1-HE.noGEN.end.gendel	percent
uq reads:	1136166	542264	47.7275%
   reads: 	1221807	572927	46.8918%
----------------
Candidate breakpoint sites in file: EB25_1-HE_depletion.xls
  reads:	56100
  uqreads:	52453
  Number of reads supporting candidate sites:	52453

Level 1 collapse of depletion sites in file: EB25_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	2405