Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EA49_1-HE.fastq.uq.polyn	EA49_1-HE.filter	percent
uq reads:	24322652	1177207	4.8400%
   reads: 	25642336	1215230	4.7392%
----------------
virus_structural_rna_repbase_filter:
  reads:	EA49_1-HE.filter	EA49_1-HE.nostrna	percent
uq reads:	1177207	1069505	90.8511%
   reads: 	1215230	1102823	90.7501%
----------------
TE_filter:
  reads:	EA49_1-HE.nostrna	EA49_1-HE.noTE	percent
uq reads:	1069505	1066123	99.6838%
   reads: 	1102823	1098256	99.5859%
----------------
match_dm6_mask_gen:1:
  reads:	EA49_1-HE.noGEN.front	EA49_1-HE.noGEN.front.gen	percent
uq reads:	1066123	581731	54.5651%
   reads: 	1098256	591950	53.8991%
----------------
match_TE:2:
  reads:	EA49_1-HE.noGEN.front	EA49_1-HE.noGEN.front.TE	percent
uq reads:	1066123	76028	7.1313%
   reads: 	1098256	78541	7.1514%
----------------
match_dm6_mask_gen:1:
  reads:	EA49_1-HE.noGEN.end	EA49_1-HE.noGEN.end.gen	percent
uq reads:	1066123	572842	53.7313%
   reads: 	1098256	583957	53.1713%
----------------
match_TE:2:
  reads:	EA49_1-HE.noGEN.end	EA49_1-HE.noGEN.end.TE	percent
uq reads:	1066123	76288	7.1556%
   reads: 	1098256	78898	7.1839%
----------------
Candidate insertion sites in file: EA49_1-HE_insert.txt
  reads:	13780
  uqreads:	13412
  Number of Candidate sites:	13412

Level 1 collapse of insertion sites in file: EA49_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	495

Level 1 annotation file: EA49_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EA49_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EA49_1-HE.noGEN.front	EA49_1-HE.noGEN.front.gendel	percent
uq reads:	1066123	581731	54.5651%
   reads: 	1098256	591950	53.8991%
----------------
match_dm6_mask_gen_del:1:
  reads:	EA49_1-HE.noGEN.end	EA49_1-HE.noGEN.end.gendel	percent
uq reads:	1066123	572842	53.7313%
   reads: 	1098256	583957	53.1713%
----------------
Candidate breakpoint sites in file: EA49_1-HE_depletion.xls
  reads:	51320
  uqreads:	50067
  Number of reads supporting candidate sites:	50067

Level 1 collapse of depletion sites in file: EA49_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3134