Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-808_75b.fastq.uq.polyn	RAL-808_75b.filter	percent
uq reads:	42438412	3226616	7.6031%
   reads: 	44011771	3418973	7.7683%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-808_75b.filter	RAL-808_75b.nostrna	percent
uq reads:	3226616	3049788	94.5197%
   reads: 	3418973	3217797	94.1159%
----------------
TE_filter:
  reads:	RAL-808_75b.nostrna	RAL-808_75b.noTE	percent
uq reads:	3049788	3035264	99.5238%
   reads: 	3217797	3202881	99.5365%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-808_75b.noGEN.front	RAL-808_75b.noGEN.front.gen	percent
uq reads:	3035264	832510	27.4279%
   reads: 	3202881	915746	28.5913%
----------------
match_TE:2:
  reads:	RAL-808_75b.noGEN.front	RAL-808_75b.noGEN.front.TE	percent
uq reads:	3035264	89297	2.9420%
   reads: 	3202881	92604	2.8913%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-808_75b.noGEN.end	RAL-808_75b.noGEN.end.gen	percent
uq reads:	3035264	654140	21.5513%
   reads: 	3202881	729368	22.7722%
----------------
match_TE:2:
  reads:	RAL-808_75b.noGEN.end	RAL-808_75b.noGEN.end.TE	percent
uq reads:	3035264	86493	2.8496%
   reads: 	3202881	89985	2.8095%
----------------
Candidate insertion sites in file: RAL-808_75b_insert.txt
  reads:	6787
  uqreads:	6741
  Number of Candidate sites:	6741

Level 1 collapse of insertion sites in file: RAL-808_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	412

Level 1 annotation file: RAL-808_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-808_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-808_75b.noGEN.front	RAL-808_75b.noGEN.front.gendel	percent
uq reads:	3035264	832510	27.4279%
   reads: 	3202881	915746	28.5913%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-808_75b.noGEN.end	RAL-808_75b.noGEN.end.gendel	percent
uq reads:	3035264	654140	21.5513%
   reads: 	3202881	729368	22.7722%
----------------
Candidate breakpoint sites in file: RAL-808_75b_depletion.xls
  reads:	14708
  uqreads:	14520
  Number of reads supporting candidate sites:	14520

Level 1 collapse of depletion sites in file: RAL-808_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1210