Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-101.fastq.uq.polyn	RAL-101.filter	percent
uq reads:	31872144	4151293	13.0248%
   reads: 	33289511	4468690	13.4237%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-101.filter	RAL-101.nostrna	percent
uq reads:	4151293	4009147	96.5759%
   reads: 	4468690	4319869	96.6697%
----------------
TE_filter:
  reads:	RAL-101.nostrna	RAL-101.noTE	percent
uq reads:	4009147	3996543	99.6856%
   reads: 	4319869	4305301	99.6628%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-101.noGEN.front	RAL-101.noGEN.front.gen	percent
uq reads:	3996543	737836	18.4619%
   reads: 	4305301	909289	21.1202%
----------------
match_TE:2:
  reads:	RAL-101.noGEN.front	RAL-101.noGEN.front.TE	percent
uq reads:	3996543	114375	2.8618%
   reads: 	4305301	115910	2.6923%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-101.noGEN.end	RAL-101.noGEN.end.gen	percent
uq reads:	3996543	771474	19.3035%
   reads: 	4305301	942971	21.9026%
----------------
match_TE:2:
  reads:	RAL-101.noGEN.end	RAL-101.noGEN.end.TE	percent
uq reads:	3996543	125286	3.1349%
   reads: 	4305301	127030	2.9505%
----------------
Candidate insertion sites in file: RAL-101_insert.txt
  reads:	5747
  uqreads:	5694
  Number of Candidate sites:	5694

Level 1 collapse of insertion sites in file: RAL-101_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	413

Level 1 annotation file: RAL-101_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-101_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-101.noGEN.front	RAL-101.noGEN.front.gendel	percent
uq reads:	3996543	748364	18.7253%
   reads: 	4305301	924698	21.4781%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-101.noGEN.end	RAL-101.noGEN.end.gendel	percent
uq reads:	3996543	784943	19.6405%
   reads: 	4305301	961499	22.3329%
----------------
Candidate breakpoint sites in file: RAL-101_depletion.xls
  reads:	13832
  uqreads:	13532
  Number of reads supporting candidate sites:	13532

Level 1 collapse of depletion sites in file: RAL-101_depletion_level1.xls
  Number of Level 1 collapsed sites:	1290