Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KR39_1-HE.fastq.uq.polyn	KR39_1-HE.filter	percent
uq reads:	51823684	2206224	4.2572%
   reads: 	59568746	2470241	4.1469%
----------------
virus_structural_rna_repbase_filter:
  reads:	KR39_1-HE.filter	KR39_1-HE.nostrna	percent
uq reads:	2206224	1948690	88.3269%
   reads: 	2470241	2172272	87.9377%
----------------
TE_filter:
  reads:	KR39_1-HE.nostrna	KR39_1-HE.noTE	percent
uq reads:	1948690	1941811	99.6470%
   reads: 	2172272	2154666	99.1895%
----------------
match_dm6_mask_gen:1:
  reads:	KR39_1-HE.noGEN.front	KR39_1-HE.noGEN.front.gen	percent
uq reads:	1941811	957574	49.3135%
   reads: 	2154666	1040623	48.2963%
----------------
match_TE:2:
  reads:	KR39_1-HE.noGEN.front	KR39_1-HE.noGEN.front.TE	percent
uq reads:	1941811	79297	4.0837%
   reads: 	2154666	86632	4.0207%
----------------
match_dm6_mask_gen:1:
  reads:	KR39_1-HE.noGEN.end	KR39_1-HE.noGEN.end.gen	percent
uq reads:	1941811	988586	50.9105%
   reads: 	2154666	1081103	50.1750%
----------------
match_TE:2:
  reads:	KR39_1-HE.noGEN.end	KR39_1-HE.noGEN.end.TE	percent
uq reads:	1941811	78892	4.0628%
   reads: 	2154666	86103	3.9961%
----------------
Candidate insertion sites in file: KR39_1-HE_insert.txt
  reads:	19426
  uqreads:	17560
  Number of Candidate sites:	17560

Level 1 collapse of insertion sites in file: KR39_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	599

Level 1 annotation file: KR39_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KR39_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KR39_1-HE.noGEN.front	KR39_1-HE.noGEN.front.gendel	percent
uq reads:	1941811	957574	49.3135%
   reads: 	2154666	1040623	48.2963%
----------------
match_dm6_mask_gen_del:1:
  reads:	KR39_1-HE.noGEN.end	KR39_1-HE.noGEN.end.gendel	percent
uq reads:	1941811	988586	50.9105%
   reads: 	2154666	1081103	50.1750%
----------------
Candidate breakpoint sites in file: KR39_1-HE_depletion.xls
  reads:	57803
  uqreads:	52190
  Number of reads supporting candidate sites:	52190

Level 1 collapse of depletion sites in file: KR39_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3305