Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-237.fastq.uq.polyn	RAL-237.filter	percent
uq reads:	32126349	4575597	14.2425%
   reads: 	34066430	5041214	14.7982%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-237.filter	RAL-237.nostrna	percent
uq reads:	4575597	4190953	91.5936%
   reads: 	5041214	4628675	91.8167%
----------------
TE_filter:
  reads:	RAL-237.nostrna	RAL-237.noTE	percent
uq reads:	4190953	4179952	99.7375%
   reads: 	4628675	4616902	99.7457%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-237.noGEN.front	RAL-237.noGEN.front.gen	percent
uq reads:	4179952	1609864	38.5139%
   reads: 	4616902	1891746	40.9744%
----------------
match_TE:2:
  reads:	RAL-237.noGEN.front	RAL-237.noGEN.front.TE	percent
uq reads:	4179952	202672	4.8487%
   reads: 	4616902	209035	4.5276%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-237.noGEN.end	RAL-237.noGEN.end.gen	percent
uq reads:	4179952	1205539	28.8410%
   reads: 	4616902	1472749	31.8991%
----------------
match_TE:2:
  reads:	RAL-237.noGEN.end	RAL-237.noGEN.end.TE	percent
uq reads:	4179952	180781	4.3250%
   reads: 	4616902	189056	4.0949%
----------------
Candidate insertion sites in file: RAL-237_insert.txt
  reads:	25457
  uqreads:	25194
  Number of Candidate sites:	25194

Level 1 collapse of insertion sites in file: RAL-237_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	316

Level 1 annotation file: RAL-237_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-237_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-237.noGEN.front	RAL-237.noGEN.front.gendel	percent
uq reads:	4179952	1609864	38.5139%
   reads: 	4616902	1891746	40.9744%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-237.noGEN.end	RAL-237.noGEN.end.gendel	percent
uq reads:	4179952	1205539	28.8410%
   reads: 	4616902	1472749	31.8991%
----------------
Candidate breakpoint sites in file: RAL-237_depletion.xls
  reads:	53737
  uqreads:	52853
  Number of reads supporting candidate sites:	52853

Level 1 collapse of depletion sites in file: RAL-237_depletion_level1.xls
  Number of Level 1 collapsed sites:	990