Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-91.fastq.uq.polyn	RAL-91.filter	percent
uq reads:	30269081	2481709	8.1988%
   reads: 	32893698	3201841	9.7339%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-91.filter	RAL-91.nostrna	percent
uq reads:	2481709	2442237	98.4095%
   reads: 	3201841	3154315	98.5157%
----------------
TE_filter:
  reads:	RAL-91.nostrna	RAL-91.noTE	percent
uq reads:	2442237	2437558	99.8084%
   reads: 	3154315	3148923	99.8291%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-91.noGEN.front	RAL-91.noGEN.front.gen	percent
uq reads:	2437558	637170	26.1397%
   reads: 	3148923	1113976	35.3764%
----------------
match_TE:2:
  reads:	RAL-91.noGEN.front	RAL-91.noGEN.front.TE	percent
uq reads:	2437558	106493	4.3688%
   reads: 	3148923	113260	3.5968%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-91.noGEN.end	RAL-91.noGEN.end.gen	percent
uq reads:	2437558	697076	28.5973%
   reads: 	3148923	1163833	36.9597%
----------------
match_TE:2:
  reads:	RAL-91.noGEN.end	RAL-91.noGEN.end.TE	percent
uq reads:	2437558	118912	4.8783%
   reads: 	3148923	126905	4.0301%
----------------
Candidate insertion sites in file: RAL-91_insert.txt
  reads:	12164
  uqreads:	12000
  Number of Candidate sites:	12000

Level 1 collapse of insertion sites in file: RAL-91_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	391

Level 1 annotation file: RAL-91_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-91_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-91.noGEN.front	RAL-91.noGEN.front.gendel	percent
uq reads:	2437558	637170	26.1397%
   reads: 	3148923	1113976	35.3764%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-91.noGEN.end	RAL-91.noGEN.end.gendel	percent
uq reads:	2437558	697076	28.5973%
   reads: 	3148923	1163833	36.9597%
----------------
Candidate breakpoint sites in file: RAL-91_depletion.xls
  reads:	26379
  uqreads:	25426
  Number of reads supporting candidate sites:	25426

Level 1 collapse of depletion sites in file: RAL-91_depletion_level1.xls
  Number of Level 1 collapsed sites:	1262