Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CK2_1-HE.fastq.uq.polyn	CK2_1-HE.filter	percent
uq reads:	38080376	1562394	4.1029%
   reads: 	40744936	1693513	4.1564%
----------------
virus_structural_rna_repbase_filter:
  reads:	CK2_1-HE.filter	CK2_1-HE.nostrna	percent
uq reads:	1562394	1241030	79.4313%
   reads: 	1693513	1311504	77.4428%
----------------
TE_filter:
  reads:	CK2_1-HE.nostrna	CK2_1-HE.noTE	percent
uq reads:	1241030	1236411	99.6278%
   reads: 	1311504	1304538	99.4689%
----------------
match_dm6_mask_gen:1:
  reads:	CK2_1-HE.noGEN.front	CK2_1-HE.noGEN.front.gen	percent
uq reads:	1236411	705953	57.0970%
   reads: 	1304538	724920	55.5691%
----------------
match_TE:2:
  reads:	CK2_1-HE.noGEN.front	CK2_1-HE.noGEN.front.TE	percent
uq reads:	1236411	99975	8.0859%
   reads: 	1304538	103816	7.9581%
----------------
match_dm6_mask_gen:1:
  reads:	CK2_1-HE.noGEN.end	CK2_1-HE.noGEN.end.gen	percent
uq reads:	1236411	574209	46.4416%
   reads: 	1304538	593870	45.5234%
----------------
match_TE:2:
  reads:	CK2_1-HE.noGEN.end	CK2_1-HE.noGEN.end.TE	percent
uq reads:	1236411	87700	7.0931%
   reads: 	1304538	91484	7.0128%
----------------
Candidate insertion sites in file: CK2_1-HE_insert.txt
  reads:	29724
  uqreads:	28255
  Number of Candidate sites:	28255

Level 1 collapse of insertion sites in file: CK2_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	688

Level 1 annotation file: CK2_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
CK2_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CK2_1-HE.noGEN.front	CK2_1-HE.noGEN.front.gendel	percent
uq reads:	1236411	705953	57.0970%
   reads: 	1304538	724920	55.5691%
----------------
match_dm6_mask_gen_del:1:
  reads:	CK2_1-HE.noGEN.end	CK2_1-HE.noGEN.end.gendel	percent
uq reads:	1236411	574209	46.4416%
   reads: 	1304538	593870	45.5234%
----------------
Candidate breakpoint sites in file: CK2_1-HE_depletion.xls
  reads:	90942
  uqreads:	87295
  Number of reads supporting candidate sites:	87295

Level 1 collapse of depletion sites in file: CK2_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	4021