Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CK1_1-HE.fastq.uq.polyn	CK1_1-HE.filter	percent
uq reads:	55780277	2546296	4.5649%
   reads: 	69370171	3546613	5.1126%
----------------
virus_structural_rna_repbase_filter:
  reads:	CK1_1-HE.filter	CK1_1-HE.nostrna	percent
uq reads:	2546296	2503830	98.3322%
   reads: 	3546613	3170502	89.3952%
----------------
TE_filter:
  reads:	CK1_1-HE.nostrna	CK1_1-HE.noTE	percent
uq reads:	2503830	2495229	99.6565%
   reads: 	3170502	3147212	99.2654%
----------------
match_dm6_mask_gen:1:
  reads:	CK1_1-HE.noGEN.front	CK1_1-HE.noGEN.front.gen	percent
uq reads:	2495229	1242612	49.7995%
   reads: 	3147212	1412699	44.8873%
----------------
match_TE:2:
  reads:	CK1_1-HE.noGEN.front	CK1_1-HE.noGEN.front.TE	percent
uq reads:	2495229	118487	4.7485%
   reads: 	3147212	138416	4.3981%
----------------
match_dm6_mask_gen:1:
  reads:	CK1_1-HE.noGEN.end	CK1_1-HE.noGEN.end.gen	percent
uq reads:	2495229	1309063	52.4626%
   reads: 	3147212	1495242	47.5101%
----------------
match_TE:2:
  reads:	CK1_1-HE.noGEN.end	CK1_1-HE.noGEN.end.TE	percent
uq reads:	2495229	121143	4.8550%
   reads: 	3147212	139874	4.4444%
----------------
Candidate insertion sites in file: CK1_1-HE_insert.txt
  reads:	21923
  uqreads:	18598
  Number of Candidate sites:	18598

Level 1 collapse of insertion sites in file: CK1_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	506

Level 1 annotation file: CK1_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
CK1_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CK1_1-HE.noGEN.front	CK1_1-HE.noGEN.front.gendel	percent
uq reads:	2495229	1242612	49.7995%
   reads: 	3147212	1412699	44.8873%
----------------
match_dm6_mask_gen_del:1:
  reads:	CK1_1-HE.noGEN.end	CK1_1-HE.noGEN.end.gendel	percent
uq reads:	2495229	1309063	52.4626%
   reads: 	3147212	1495242	47.5101%
----------------
Candidate breakpoint sites in file: CK1_1-HE_depletion.xls
  reads:	108237
  uqreads:	96944
  Number of reads supporting candidate sites:	96944

Level 1 collapse of depletion sites in file: CK1_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3742