Insertion Pipeline
Bowtie2_wholegenome:
  reads:	GA129_1-HE.fastq.uq.polyn	GA129_1-HE.filter	percent
uq reads:	68749746	2685475	3.9062%
   reads: 	81847692	3120247	3.8123%
----------------
virus_structural_rna_repbase_filter:
  reads:	GA129_1-HE.filter	GA129_1-HE.nostrna	percent
uq reads:	2685475	2660583	99.0731%
   reads: 	3120247	3077355	98.6254%
----------------
TE_filter:
  reads:	GA129_1-HE.nostrna	GA129_1-HE.noTE	percent
uq reads:	2660583	2650719	99.6293%
   reads: 	3077355	3055691	99.2960%
----------------
match_dm6_mask_gen:1:
  reads:	GA129_1-HE.noGEN.front	GA129_1-HE.noGEN.front.gen	percent
uq reads:	2650719	1294465	48.8345%
   reads: 	3055691	1452133	47.5222%
----------------
match_TE:2:
  reads:	GA129_1-HE.noGEN.front	GA129_1-HE.noGEN.front.TE	percent
uq reads:	2650719	104446	3.9403%
   reads: 	3055691	117508	3.8455%
----------------
match_dm6_mask_gen:1:
  reads:	GA129_1-HE.noGEN.end	GA129_1-HE.noGEN.end.gen	percent
uq reads:	2650719	1348080	50.8571%
   reads: 	3055691	1522692	49.8313%
----------------
match_TE:2:
  reads:	GA129_1-HE.noGEN.end	GA129_1-HE.noGEN.end.TE	percent
uq reads:	2650719	102766	3.8769%
   reads: 	3055691	115394	3.7764%
----------------
Candidate insertion sites in file: GA129_1-HE_insert.txt
  reads:	21303
  uqreads:	18584
  Number of Candidate sites:	18584

Level 1 collapse of insertion sites in file: GA129_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	542

Level 1 annotation file: GA129_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
GA129_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	GA129_1-HE.noGEN.front	GA129_1-HE.noGEN.front.gendel	percent
uq reads:	2650719	1294465	48.8345%
   reads: 	3055691	1452133	47.5222%
----------------
match_dm6_mask_gen_del:1:
  reads:	GA129_1-HE.noGEN.end	GA129_1-HE.noGEN.end.gendel	percent
uq reads:	2650719	1348080	50.8571%
   reads: 	3055691	1522692	49.8313%
----------------
Candidate breakpoint sites in file: GA129_1-HE_depletion.xls
  reads:	83739
  uqreads:	72964
  Number of reads supporting candidate sites:	72964

Level 1 collapse of depletion sites in file: GA129_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3872