Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-721.fastq.uq.polyn	RAL-721.filter	percent
uq reads:	31841296	3851752	12.0967%
   reads: 	33123393	4215949	12.7280%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-721.filter	RAL-721.nostrna	percent
uq reads:	3851752	2397246	62.2378%
   reads: 	4215949	2561462	60.7565%
----------------
TE_filter:
  reads:	RAL-721.nostrna	RAL-721.noTE	percent
uq reads:	2397246	2383729	99.4361%
   reads: 	2561462	2546671	99.4226%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-721.noGEN.front	RAL-721.noGEN.front.gen	percent
uq reads:	2383729	624352	26.1922%
   reads: 	2546671	713470	28.0158%
----------------
match_TE:2:
  reads:	RAL-721.noGEN.front	RAL-721.noGEN.front.TE	percent
uq reads:	2383729	73746	3.0937%
   reads: 	2546671	75233	2.9542%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-721.noGEN.end	RAL-721.noGEN.end.gen	percent
uq reads:	2383729	522723	21.9288%
   reads: 	2546671	607317	23.8475%
----------------
match_TE:2:
  reads:	RAL-721.noGEN.end	RAL-721.noGEN.end.TE	percent
uq reads:	2383729	72497	3.0413%
   reads: 	2546671	74462	2.9239%
----------------
Candidate insertion sites in file: RAL-721_insert.txt
  reads:	6420
  uqreads:	6345
  Number of Candidate sites:	6345

Level 1 collapse of insertion sites in file: RAL-721_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	412

Level 1 annotation file: RAL-721_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-721_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-721.noGEN.front	RAL-721.noGEN.front.gendel	percent
uq reads:	2383729	624352	26.1922%
   reads: 	2546671	713470	28.0158%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-721.noGEN.end	RAL-721.noGEN.end.gendel	percent
uq reads:	2383729	522723	21.9288%
   reads: 	2546671	607317	23.8475%
----------------
Candidate breakpoint sites in file: RAL-721_depletion.xls
  reads:	14085
  uqreads:	13700
  Number of reads supporting candidate sites:	13700

Level 1 collapse of depletion sites in file: RAL-721_depletion_level1.xls
  Number of Level 1 collapsed sites:	1252