Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-235.fastq.uq.polyn	RAL-235.filter	percent
uq reads:	36033643	2287192	6.3474%
   reads: 	37498892	2568699	6.8501%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-235.filter	RAL-235.nostrna	percent
uq reads:	2287192	2150823	94.0377%
   reads: 	2568699	2386322	92.9000%
----------------
TE_filter:
  reads:	RAL-235.nostrna	RAL-235.noTE	percent
uq reads:	2150823	2139700	99.4828%
   reads: 	2386322	2374625	99.5098%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-235.noGEN.front	RAL-235.noGEN.front.gen	percent
uq reads:	2139700	678996	31.7332%
   reads: 	2374625	752945	31.7080%
----------------
match_TE:2:
  reads:	RAL-235.noGEN.front	RAL-235.noGEN.front.TE	percent
uq reads:	2139700	99513	4.6508%
   reads: 	2374625	110070	4.6353%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-235.noGEN.end	RAL-235.noGEN.end.gen	percent
uq reads:	2139700	583051	27.2492%
   reads: 	2374625	653746	27.5305%
----------------
match_TE:2:
  reads:	RAL-235.noGEN.end	RAL-235.noGEN.end.TE	percent
uq reads:	2139700	91078	4.2566%
   reads: 	2374625	100832	4.2462%
----------------
Candidate insertion sites in file: RAL-235_insert.txt
  reads:	13251
  uqreads:	13014
  Number of Candidate sites:	13014

Level 1 collapse of insertion sites in file: RAL-235_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	569

Level 1 annotation file: RAL-235_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-235_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-235.noGEN.front	RAL-235.noGEN.front.gendel	percent
uq reads:	2139700	690424	32.2673%
   reads: 	2374625	766522	32.2797%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-235.noGEN.end	RAL-235.noGEN.end.gendel	percent
uq reads:	2139700	592207	27.6771%
   reads: 	2374625	664751	27.9939%
----------------
Candidate breakpoint sites in file: RAL-235_depletion.xls
  reads:	31804
  uqreads:	31409
  Number of reads supporting candidate sites:	31409

Level 1 collapse of depletion sites in file: RAL-235_depletion_level1.xls
  Number of Level 1 collapsed sites:	2703