Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-732.fastq.uq.polyn	RAL-732.filter	percent
uq reads:	38593313	5511772	14.2817%
   reads: 	41309126	6117061	14.8080%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-732.filter	RAL-732.nostrna	percent
uq reads:	5511772	5473126	99.2988%
   reads: 	6117061	6054252	98.9732%
----------------
TE_filter:
  reads:	RAL-732.nostrna	RAL-732.noTE	percent
uq reads:	5473126	5465034	99.8522%
   reads: 	6054252	6044824	99.8443%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-732.noGEN.front	RAL-732.noGEN.front.gen	percent
uq reads:	5465034	1679054	30.7236%
   reads: 	6044824	1977885	32.7203%
----------------
match_TE:2:
  reads:	RAL-732.noGEN.front	RAL-732.noGEN.front.TE	percent
uq reads:	5465034	243989	4.4645%
   reads: 	6044824	249873	4.1337%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-732.noGEN.end	RAL-732.noGEN.end.gen	percent
uq reads:	5465034	545682	9.9850%
   reads: 	6044824	810073	13.4011%
----------------
match_TE:2:
  reads:	RAL-732.noGEN.end	RAL-732.noGEN.end.TE	percent
uq reads:	5465034	123417	2.2583%
   reads: 	6044824	131333	2.1727%
----------------
Candidate insertion sites in file: RAL-732_insert.txt
  reads:	9293
  uqreads:	9069
  Number of Candidate sites:	9069

Level 1 collapse of insertion sites in file: RAL-732_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	484

Level 1 annotation file: RAL-732_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-732_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-732.noGEN.front	RAL-732.noGEN.front.gendel	percent
uq reads:	5465034	1679054	30.7236%
   reads: 	6044824	1977885	32.7203%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-732.noGEN.end	RAL-732.noGEN.end.gendel	percent
uq reads:	5465034	545682	9.9850%
   reads: 	6044824	810073	13.4011%
----------------
Candidate breakpoint sites in file: RAL-732_depletion.xls
  reads:	21117
  uqreads:	19810
  Number of reads supporting candidate sites:	19810

Level 1 collapse of depletion sites in file: RAL-732_depletion_level1.xls
  Number of Level 1 collapsed sites:	1955