Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RC1_1-HE.fastq.uq.polyn	RC1_1-HE.filter	percent
uq reads:	46320608	2452552	5.2947%
   reads: 	51240263	2631353	5.1353%
----------------
virus_structural_rna_repbase_filter:
  reads:	RC1_1-HE.filter	RC1_1-HE.nostrna	percent
uq reads:	2452552	2114688	86.2240%
   reads: 	2631353	2263403	86.0167%
----------------
TE_filter:
  reads:	RC1_1-HE.nostrna	RC1_1-HE.noTE	percent
uq reads:	2114688	2105776	99.5786%
   reads: 	2263403	2247049	99.2775%
----------------
match_dm6_mask_gen:1:
  reads:	RC1_1-HE.noGEN.front	RC1_1-HE.noGEN.front.gen	percent
uq reads:	2105776	1014504	48.1772%
   reads: 	2247049	1071177	47.6704%
----------------
match_TE:2:
  reads:	RC1_1-HE.noGEN.front	RC1_1-HE.noGEN.front.TE	percent
uq reads:	2105776	75843	3.6017%
   reads: 	2247049	81272	3.6168%
----------------
match_dm6_mask_gen:1:
  reads:	RC1_1-HE.noGEN.end	RC1_1-HE.noGEN.end.gen	percent
uq reads:	2105776	907027	43.0733%
   reads: 	2247049	970720	43.1998%
----------------
match_TE:2:
  reads:	RC1_1-HE.noGEN.end	RC1_1-HE.noGEN.end.TE	percent
uq reads:	2105776	65519	3.1114%
   reads: 	2247049	71027	3.1609%
----------------
Candidate insertion sites in file: RC1_1-HE_insert.txt
  reads:	12636
  uqreads:	11621
  Number of Candidate sites:	11621

Level 1 collapse of insertion sites in file: RC1_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	486

Level 1 annotation file: RC1_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
RC1_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RC1_1-HE.noGEN.front	RC1_1-HE.noGEN.front.gendel	percent
uq reads:	2105776	1014504	48.1772%
   reads: 	2247049	1071177	47.6704%
----------------
match_dm6_mask_gen_del:1:
  reads:	RC1_1-HE.noGEN.end	RC1_1-HE.noGEN.end.gendel	percent
uq reads:	2105776	907027	43.0733%
   reads: 	2247049	970720	43.1998%
----------------
Candidate breakpoint sites in file: RC1_1-HE_depletion.xls
  reads:	47590
  uqreads:	43862
  Number of reads supporting candidate sites:	43862

Level 1 collapse of depletion sites in file: RC1_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3284