Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SF428_1-HE.fastq.uq.polyn	SF428_1-HE.filter	percent
uq reads:	23826841	1120661	4.7034%
   reads: 	24985354	1151846	4.6101%
----------------
virus_structural_rna_repbase_filter:
  reads:	SF428_1-HE.filter	SF428_1-HE.nostrna	percent
uq reads:	1120661	999927	89.2265%
   reads: 	1151846	1026091	89.0823%
----------------
TE_filter:
  reads:	SF428_1-HE.nostrna	SF428_1-HE.noTE	percent
uq reads:	999927	992627	99.2699%
   reads: 	1026091	1017118	99.1255%
----------------
match_dm6_mask_gen:1:
  reads:	SF428_1-HE.noGEN.front	SF428_1-HE.noGEN.front.gen	percent
uq reads:	992627	439582	44.2847%
   reads: 	1017118	446046	43.8539%
----------------
match_TE:2:
  reads:	SF428_1-HE.noGEN.front	SF428_1-HE.noGEN.front.TE	percent
uq reads:	992627	103523	10.4292%
   reads: 	1017118	106510	10.4717%
----------------
match_dm6_mask_gen:1:
  reads:	SF428_1-HE.noGEN.end	SF428_1-HE.noGEN.end.gen	percent
uq reads:	992627	457029	46.0424%
   reads: 	1017118	463893	45.6086%
----------------
match_TE:2:
  reads:	SF428_1-HE.noGEN.end	SF428_1-HE.noGEN.end.TE	percent
uq reads:	992627	108893	10.9702%
   reads: 	1017118	111960	11.0076%
----------------
Candidate insertion sites in file: SF428_1-HE_insert.txt
  reads:	12263
  uqreads:	12020
  Number of Candidate sites:	12020

Level 1 collapse of insertion sites in file: SF428_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	429

Level 1 annotation file: SF428_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SF428_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SF428_1-HE.noGEN.front	SF428_1-HE.noGEN.front.gendel	percent
uq reads:	992627	439582	44.2847%
   reads: 	1017118	446046	43.8539%
----------------
match_dm6_mask_gen_del:1:
  reads:	SF428_1-HE.noGEN.end	SF428_1-HE.noGEN.end.gendel	percent
uq reads:	992627	457029	46.0424%
   reads: 	1017118	463893	45.6086%
----------------
Candidate breakpoint sites in file: SF428_1-HE_depletion.xls
  reads:	35089
  uqreads:	34393
  Number of reads supporting candidate sites:	34393

Level 1 collapse of depletion sites in file: SF428_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	2687