Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-790.fastq.uq.polyn	RAL-790.filter	percent
uq reads:	32267623	3654998	11.3271%
   reads: 	34754303	4373988	12.5855%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-790.filter	RAL-790.nostrna	percent
uq reads:	3654998	2637680	72.1664%
   reads: 	4373988	3231068	73.8701%
----------------
TE_filter:
  reads:	RAL-790.nostrna	RAL-790.noTE	percent
uq reads:	2637680	2623501	99.4624%
   reads: 	3231068	3215275	99.5112%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-790.noGEN.front	RAL-790.noGEN.front.gen	percent
uq reads:	2623501	614995	23.4418%
   reads: 	3215275	758716	23.5972%
----------------
match_TE:2:
  reads:	RAL-790.noGEN.front	RAL-790.noGEN.front.TE	percent
uq reads:	2623501	86663	3.3033%
   reads: 	3215275	95438	2.9683%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-790.noGEN.end	RAL-790.noGEN.end.gen	percent
uq reads:	2623501	532411	20.2939%
   reads: 	3215275	667526	20.7611%
----------------
match_TE:2:
  reads:	RAL-790.noGEN.end	RAL-790.noGEN.end.TE	percent
uq reads:	2623501	81545	3.1083%
   reads: 	3215275	90501	2.8147%
----------------
Candidate insertion sites in file: RAL-790_insert.txt
  reads:	11753
  uqreads:	11521
  Number of Candidate sites:	11521

Level 1 collapse of insertion sites in file: RAL-790_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	505

Level 1 annotation file: RAL-790_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-790_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-790.noGEN.front	RAL-790.noGEN.front.gendel	percent
uq reads:	2623501	626213	23.8694%
   reads: 	3215275	774762	24.0963%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-790.noGEN.end	RAL-790.noGEN.end.gendel	percent
uq reads:	2623501	541014	20.6218%
   reads: 	3215275	680360	21.1602%
----------------
Candidate breakpoint sites in file: RAL-790_depletion.xls
  reads:	30092
  uqreads:	29450
  Number of reads supporting candidate sites:	29450

Level 1 collapse of depletion sites in file: RAL-790_depletion_level1.xls
  Number of Level 1 collapsed sites:	2587