Insertion Pipeline
Bowtie2_wholegenome:
  reads:	NG10N_1-HE.fastq.uq.polyn	NG10N_1-HE.filter	percent
uq reads:	58979564	2647928	4.4896%
   reads: 	66299819	2915656	4.3977%
----------------
virus_structural_rna_repbase_filter:
  reads:	NG10N_1-HE.filter	NG10N_1-HE.nostrna	percent
uq reads:	2647928	2622315	99.0327%
   reads: 	2915656	2880357	98.7893%
----------------
TE_filter:
  reads:	NG10N_1-HE.nostrna	NG10N_1-HE.noTE	percent
uq reads:	2622315	2613030	99.6459%
   reads: 	2880357	2862947	99.3956%
----------------
match_dm6_mask_gen:1:
  reads:	NG10N_1-HE.noGEN.front	NG10N_1-HE.noGEN.front.gen	percent
uq reads:	2613030	1265629	48.4353%
   reads: 	2862947	1373038	47.9589%
----------------
match_TE:2:
  reads:	NG10N_1-HE.noGEN.front	NG10N_1-HE.noGEN.front.TE	percent
uq reads:	2613030	94165	3.6037%
   reads: 	2862947	101897	3.5592%
----------------
match_dm6_mask_gen:1:
  reads:	NG10N_1-HE.noGEN.end	NG10N_1-HE.noGEN.end.gen	percent
uq reads:	2613030	1271993	48.6789%
   reads: 	2862947	1389881	48.5472%
----------------
match_TE:2:
  reads:	NG10N_1-HE.noGEN.end	NG10N_1-HE.noGEN.end.TE	percent
uq reads:	2613030	92589	3.5434%
   reads: 	2862947	100000	3.4929%
----------------
Candidate insertion sites in file: NG10N_1-HE_insert.txt
  reads:	15427
  uqreads:	14095
  Number of Candidate sites:	14095

Level 1 collapse of insertion sites in file: NG10N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	433

Level 1 annotation file: NG10N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
NG10N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	NG10N_1-HE.noGEN.front	NG10N_1-HE.noGEN.front.gendel	percent
uq reads:	2613030	1265629	48.4353%
   reads: 	2862947	1373038	47.9589%
----------------
match_dm6_mask_gen_del:1:
  reads:	NG10N_1-HE.noGEN.end	NG10N_1-HE.noGEN.end.gendel	percent
uq reads:	2613030	1271993	48.6789%
   reads: 	2862947	1389881	48.5472%
----------------
Candidate breakpoint sites in file: NG10N_1-HE_depletion.xls
  reads:	68242
  uqreads:	61013
  Number of reads supporting candidate sites:	61013

Level 1 collapse of depletion sites in file: NG10N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3796