Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-158.fastq.uq.polyn	RAL-158.filter	percent
uq reads:	29686765	2914920	9.8189%
   reads: 	30760216	3175415	10.3231%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-158.filter	RAL-158.nostrna	percent
uq reads:	2914920	2864995	98.2873%
   reads: 	3175415	3123081	98.3519%
----------------
TE_filter:
  reads:	RAL-158.nostrna	RAL-158.noTE	percent
uq reads:	2864995	2850178	99.4828%
   reads: 	3123081	3107534	99.5022%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-158.noGEN.front	RAL-158.noGEN.front.gen	percent
uq reads:	2850178	521157	18.2851%
   reads: 	3107534	680365	21.8940%
----------------
match_TE:2:
  reads:	RAL-158.noGEN.front	RAL-158.noGEN.front.TE	percent
uq reads:	2850178	59434	2.0853%
   reads: 	3107534	60788	1.9561%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-158.noGEN.end	RAL-158.noGEN.end.gen	percent
uq reads:	2850178	405431	14.2248%
   reads: 	3107534	550536	17.7162%
----------------
match_TE:2:
  reads:	RAL-158.noGEN.end	RAL-158.noGEN.end.TE	percent
uq reads:	2850178	54747	1.9208%
   reads: 	3107534	56175	1.8077%
----------------
Candidate insertion sites in file: RAL-158_insert.txt
  reads:	4217
  uqreads:	4187
  Number of Candidate sites:	4187

Level 1 collapse of insertion sites in file: RAL-158_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	318

Level 1 annotation file: RAL-158_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-158_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-158.noGEN.front	RAL-158.noGEN.front.gendel	percent
uq reads:	2850178	521157	18.2851%
   reads: 	3107534	680365	21.8940%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-158.noGEN.end	RAL-158.noGEN.end.gendel	percent
uq reads:	2850178	405431	14.2248%
   reads: 	3107534	550536	17.7162%
----------------
Candidate breakpoint sites in file: RAL-158_depletion.xls
  reads:	9784
  uqreads:	9666
  Number of reads supporting candidate sites:	9666

Level 1 collapse of depletion sites in file: RAL-158_depletion_level1.xls
  Number of Level 1 collapsed sites:	784