Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RC5_1-HE.fastq.uq.polyn	RC5_1-HE.filter	percent
uq reads:	46987287	6119072	13.0228%
   reads: 	57978393	12187400	21.0206%
----------------
virus_structural_rna_repbase_filter:
  reads:	RC5_1-HE.filter	RC5_1-HE.nostrna	percent
uq reads:	6119072	2093677	34.2156%
   reads: 	12187400	2226342	18.2676%
----------------
TE_filter:
  reads:	RC5_1-HE.nostrna	RC5_1-HE.noTE	percent
uq reads:	2093677	2077184	99.2122%
   reads: 	2226342	2203929	98.9933%
----------------
match_dm6_mask_gen:1:
  reads:	RC5_1-HE.noGEN.front	RC5_1-HE.noGEN.front.gen	percent
uq reads:	2077184	861640	41.4812%
   reads: 	2203929	906532	41.1325%
----------------
match_TE:2:
  reads:	RC5_1-HE.noGEN.front	RC5_1-HE.noGEN.front.TE	percent
uq reads:	2077184	110629	5.3259%
   reads: 	2203929	120366	5.4614%
----------------
match_dm6_mask_gen:1:
  reads:	RC5_1-HE.noGEN.end	RC5_1-HE.noGEN.end.gen	percent
uq reads:	2077184	910846	43.8500%
   reads: 	2203929	960420	43.5776%
----------------
match_TE:2:
  reads:	RC5_1-HE.noGEN.end	RC5_1-HE.noGEN.end.TE	percent
uq reads:	2077184	112657	5.4235%
   reads: 	2203929	122484	5.5575%
----------------
Candidate insertion sites in file: RC5_1-HE_insert.txt
  reads:	12894
  uqreads:	12024
  Number of Candidate sites:	12024

Level 1 collapse of insertion sites in file: RC5_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	463

Level 1 annotation file: RC5_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
RC5_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RC5_1-HE.noGEN.front	RC5_1-HE.noGEN.front.gendel	percent
uq reads:	2077184	861640	41.4812%
   reads: 	2203929	906532	41.1325%
----------------
match_dm6_mask_gen_del:1:
  reads:	RC5_1-HE.noGEN.end	RC5_1-HE.noGEN.end.gendel	percent
uq reads:	2077184	910846	43.8500%
   reads: 	2203929	960420	43.5776%
----------------
Candidate breakpoint sites in file: RC5_1-HE_depletion.xls
  reads:	41230
  uqreads:	38514
  Number of reads supporting candidate sites:	38514

Level 1 collapse of depletion sites in file: RC5_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3032