Insertion Pipeline
Bowtie2_wholegenome:
  reads:	GU10_1-HE.fastq.uq.polyn	GU10_1-HE.filter	percent
uq reads:	58103232	2337969	4.0238%
   reads: 	65682052	2625218	3.9969%
----------------
virus_structural_rna_repbase_filter:
  reads:	GU10_1-HE.filter	GU10_1-HE.nostrna	percent
uq reads:	2337969	2308023	98.7191%
   reads: 	2625218	2568148	97.8261%
----------------
TE_filter:
  reads:	GU10_1-HE.nostrna	GU10_1-HE.noTE	percent
uq reads:	2308023	2297999	99.5657%
   reads: 	2568148	2541536	98.9638%
----------------
match_dm6_mask_gen:1:
  reads:	GU10_1-HE.noGEN.front	GU10_1-HE.noGEN.front.gen	percent
uq reads:	2297999	1123803	48.9035%
   reads: 	2541536	1217605	47.9082%
----------------
match_TE:2:
  reads:	GU10_1-HE.noGEN.front	GU10_1-HE.noGEN.front.TE	percent
uq reads:	2297999	89462	3.8930%
   reads: 	2541536	97411	3.8328%
----------------
match_dm6_mask_gen:1:
  reads:	GU10_1-HE.noGEN.end	GU10_1-HE.noGEN.end.gen	percent
uq reads:	2297999	1161856	50.5595%
   reads: 	2541536	1267123	49.8566%
----------------
match_TE:2:
  reads:	GU10_1-HE.noGEN.end	GU10_1-HE.noGEN.end.TE	percent
uq reads:	2297999	88605	3.8557%
   reads: 	2541536	96459	3.7953%
----------------
Candidate insertion sites in file: GU10_1-HE_insert.txt
  reads:	16590
  uqreads:	15037
  Number of Candidate sites:	15037

Level 1 collapse of insertion sites in file: GU10_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	496

Level 1 annotation file: GU10_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
GU10_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	GU10_1-HE.noGEN.front	GU10_1-HE.noGEN.front.gendel	percent
uq reads:	2297999	1123803	48.9035%
   reads: 	2541536	1217605	47.9082%
----------------
match_dm6_mask_gen_del:1:
  reads:	GU10_1-HE.noGEN.end	GU10_1-HE.noGEN.end.gendel	percent
uq reads:	2297999	1161856	50.5595%
   reads: 	2541536	1267123	49.8566%
----------------
Candidate breakpoint sites in file: GU10_1-HE_depletion.xls
  reads:	69772
  uqreads:	63249
  Number of reads supporting candidate sites:	63249

Level 1 collapse of depletion sites in file: GU10_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3849