Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-228.fastq.uq.polyn	RAL-228.filter	percent
uq reads:	26734635	1636489	6.1212%
   reads: 	28700016	2111406	7.3568%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-228.filter	RAL-228.nostrna	percent
uq reads:	1636489	1602587	97.9284%
   reads: 	2111406	2069574	98.0188%
----------------
TE_filter:
  reads:	RAL-228.nostrna	RAL-228.noTE	percent
uq reads:	1602587	1593958	99.4616%
   reads: 	2069574	2059691	99.5225%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-228.noGEN.front	RAL-228.noGEN.front.gen	percent
uq reads:	1593958	528234	33.1398%
   reads: 	2059691	827075	40.1553%
----------------
match_TE:2:
  reads:	RAL-228.noGEN.front	RAL-228.noGEN.front.TE	percent
uq reads:	1593958	81957	5.1417%
   reads: 	2059691	85399	4.1462%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-228.noGEN.end	RAL-228.noGEN.end.gen	percent
uq reads:	1593958	296059	18.5738%
   reads: 	2059691	584497	28.3779%
----------------
match_TE:2:
  reads:	RAL-228.noGEN.end	RAL-228.noGEN.end.TE	percent
uq reads:	1593958	55014	3.4514%
   reads: 	2059691	58761	2.8529%
----------------
Candidate insertion sites in file: RAL-228_insert.txt
  reads:	5236
  uqreads:	5146
  Number of Candidate sites:	5146

Level 1 collapse of insertion sites in file: RAL-228_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	411

Level 1 annotation file: RAL-228_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-228_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-228.noGEN.front	RAL-228.noGEN.front.gendel	percent
uq reads:	1593958	528234	33.1398%
   reads: 	2059691	827075	40.1553%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-228.noGEN.end	RAL-228.noGEN.end.gendel	percent
uq reads:	1593958	296059	18.5738%
   reads: 	2059691	584497	28.3779%
----------------
Candidate breakpoint sites in file: RAL-228_depletion.xls
  reads:	12922
  uqreads:	12322
  Number of reads supporting candidate sites:	12322

Level 1 collapse of depletion sites in file: RAL-228_depletion_level1.xls
  Number of Level 1 collapsed sites:	1223