Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-217.fastq.uq.polyn	RAL-217.filter	percent
uq reads:	29082218	1658527	5.7029%
   reads: 	31037869	2088421	6.7286%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-217.filter	RAL-217.nostrna	percent
uq reads:	1658527	1617657	97.5358%
   reads: 	2088421	2042063	97.7802%
----------------
TE_filter:
  reads:	RAL-217.nostrna	RAL-217.noTE	percent
uq reads:	1617657	1610862	99.5799%
   reads: 	2042063	2033643	99.5877%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-217.noGEN.front	RAL-217.noGEN.front.gen	percent
uq reads:	1610862	400745	24.8777%
   reads: 	2033643	685914	33.7283%
----------------
match_TE:2:
  reads:	RAL-217.noGEN.front	RAL-217.noGEN.front.TE	percent
uq reads:	1610862	62150	3.8582%
   reads: 	2033643	65368	3.2143%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-217.noGEN.end	RAL-217.noGEN.end.gen	percent
uq reads:	1610862	342025	21.2324%
   reads: 	2033643	620308	30.5023%
----------------
match_TE:2:
  reads:	RAL-217.noGEN.end	RAL-217.noGEN.end.TE	percent
uq reads:	1610862	60203	3.7373%
   reads: 	2033643	63443	3.1197%
----------------
Candidate insertion sites in file: RAL-217_insert.txt
  reads:	4880
  uqreads:	4790
  Number of Candidate sites:	4790

Level 1 collapse of insertion sites in file: RAL-217_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	329

Level 1 annotation file: RAL-217_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-217_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-217.noGEN.front	RAL-217.noGEN.front.gendel	percent
uq reads:	1610862	400745	24.8777%
   reads: 	2033643	685914	33.7283%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-217.noGEN.end	RAL-217.noGEN.end.gendel	percent
uq reads:	1610862	342025	21.2324%
   reads: 	2033643	620308	30.5023%
----------------
Candidate breakpoint sites in file: RAL-217_depletion.xls
  reads:	12904
  uqreads:	12399
  Number of reads supporting candidate sites:	12399

Level 1 collapse of depletion sites in file: RAL-217_depletion_level1.xls
  Number of Level 1 collapsed sites:	1173