Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-821_100b.fastq.uq.polyn	RAL-821_100b.filter	percent
uq reads:	112261216	13931702	12.4101%
   reads: 	131329385	18048333	13.7428%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-821_100b.filter	RAL-821_100b.nostrna	percent
uq reads:	13931702	10735536	77.0583%
   reads: 	18048333	13263213	73.4872%
----------------
TE_filter:
  reads:	RAL-821_100b.nostrna	RAL-821_100b.noTE	percent
uq reads:	10735536	10710520	99.7670%
   reads: 	13263213	13222749	99.6949%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-821_100b.noGEN.front	RAL-821_100b.noGEN.front.gen	percent
uq reads:	10710520	1693898	15.8153%
   reads: 	13222749	2868904	21.6967%
----------------
match_TE:2:
  reads:	RAL-821_100b.noGEN.front	RAL-821_100b.noGEN.front.TE	percent
uq reads:	10710520	315519	2.9459%
   reads: 	13222749	357730	2.7054%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-821_100b.noGEN.end	RAL-821_100b.noGEN.end.gen	percent
uq reads:	10710520	1231964	11.5024%
   reads: 	13222749	2402752	18.1713%
----------------
match_TE:2:
  reads:	RAL-821_100b.noGEN.end	RAL-821_100b.noGEN.end.TE	percent
uq reads:	10710520	258023	2.4091%
   reads: 	13222749	299378	2.2641%
----------------
Candidate insertion sites in file: RAL-821_100b_insert.txt
  reads:	42991
  uqreads:	39956
  Number of Candidate sites:	39956

Level 1 collapse of insertion sites in file: RAL-821_100b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	781

Level 1 annotation file: RAL-821_100b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-821_100b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-821_100b.noGEN.front	RAL-821_100b.noGEN.front.gendel	percent
uq reads:	10710520	1693898	15.8153%
   reads: 	13222749	2868904	21.6967%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-821_100b.noGEN.end	RAL-821_100b.noGEN.end.gendel	percent
uq reads:	10710520	1231964	11.5024%
   reads: 	13222749	2402752	18.1713%
----------------
Candidate breakpoint sites in file: RAL-821_100b_depletion.xls
  reads:	106774
  uqreads:	97977
  Number of reads supporting candidate sites:	97977

Level 1 collapse of depletion sites in file: RAL-821_100b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4696