Insertion Pipeline
Bowtie2_wholegenome:
  reads:	GU2_1-HE.fastq.uq.polyn	GU2_1-HE.filter	percent
uq reads:	56658066	2497458	4.4079%
   reads: 	65139843	2873614	4.4115%
----------------
virus_structural_rna_repbase_filter:
  reads:	GU2_1-HE.filter	GU2_1-HE.nostrna	percent
uq reads:	2497458	2461535	98.5616%
   reads: 	2873614	2772939	96.4966%
----------------
TE_filter:
  reads:	GU2_1-HE.nostrna	GU2_1-HE.noTE	percent
uq reads:	2461535	2452126	99.6178%
   reads: 	2772939	2748629	99.1233%
----------------
match_dm6_mask_gen:1:
  reads:	GU2_1-HE.noGEN.front	GU2_1-HE.noGEN.front.gen	percent
uq reads:	2452126	1212973	49.4662%
   reads: 	2748629	1323379	48.1469%
----------------
match_TE:2:
  reads:	GU2_1-HE.noGEN.front	GU2_1-HE.noGEN.front.TE	percent
uq reads:	2452126	87275	3.5592%
   reads: 	2748629	95673	3.4808%
----------------
match_dm6_mask_gen:1:
  reads:	GU2_1-HE.noGEN.end	GU2_1-HE.noGEN.end.gen	percent
uq reads:	2452126	1233097	50.2869%
   reads: 	2748629	1354938	49.2950%
----------------
match_TE:2:
  reads:	GU2_1-HE.noGEN.end	GU2_1-HE.noGEN.end.TE	percent
uq reads:	2452126	86939	3.5455%
   reads: 	2748629	94989	3.4559%
----------------
Candidate insertion sites in file: GU2_1-HE_insert.txt
  reads:	18649
  uqreads:	16655
  Number of Candidate sites:	16655

Level 1 collapse of insertion sites in file: GU2_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	511

Level 1 annotation file: GU2_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
GU2_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	GU2_1-HE.noGEN.front	GU2_1-HE.noGEN.front.gendel	percent
uq reads:	2452126	1212973	49.4662%
   reads: 	2748629	1323379	48.1469%
----------------
match_dm6_mask_gen_del:1:
  reads:	GU2_1-HE.noGEN.end	GU2_1-HE.noGEN.end.gendel	percent
uq reads:	2452126	1233097	50.2869%
   reads: 	2748629	1354938	49.2950%
----------------
Candidate breakpoint sites in file: GU2_1-HE_depletion.xls
  reads:	71023
  uqreads:	63796
  Number of reads supporting candidate sites:	63796

Level 1 collapse of depletion sites in file: GU2_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3731