Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EG40N.fastq.uq.polyn	EG40N.filter	percent
uq reads:	20236886	1095036	5.4111%
   reads: 	21281550	1221460	5.7395%
----------------
virus_structural_rna_repbase_filter:
  reads:	EG40N.filter	EG40N.nostrna	percent
uq reads:	1095036	1058971	96.7065%
   reads: 	1221460	1168364	95.6531%
----------------
TE_filter:
  reads:	EG40N.nostrna	EG40N.noTE	percent
uq reads:	1058971	1049656	99.1204%
   reads: 	1168364	1157519	99.0718%
----------------
match_dm6_mask_gen:1:
  reads:	EG40N.noGEN.front	EG40N.noGEN.front.gen	percent
uq reads:	1049656	305264	29.0823%
   reads: 	1157519	335640	28.9965%
----------------
match_TE:2:
  reads:	EG40N.noGEN.front	EG40N.noGEN.front.TE	percent
uq reads:	1049656	47436	4.5192%
   reads: 	1157519	48586	4.1974%
----------------
match_dm6_mask_gen:1:
  reads:	EG40N.noGEN.end	EG40N.noGEN.end.gen	percent
uq reads:	1049656	322245	30.7001%
   reads: 	1157519	353649	30.5523%
----------------
match_TE:2:
  reads:	EG40N.noGEN.end	EG40N.noGEN.end.TE	percent
uq reads:	1049656	49717	4.7365%
   reads: 	1157519	51038	4.4093%
----------------
Candidate insertion sites in file: EG40N_insert.txt
  reads:	6959
  uqreads:	6881
  Number of Candidate sites:	6881

Level 1 collapse of insertion sites in file: EG40N_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	557

Level 1 annotation file: EG40N_level1siteannotation.xls
Insertion sites in fixed bin:
EG40N_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EG40N.noGEN.front	EG40N.noGEN.front.gendel	percent
uq reads:	1049656	305264	29.0823%
   reads: 	1157519	335640	28.9965%
----------------
match_dm6_mask_gen_del:1:
  reads:	EG40N.noGEN.end	EG40N.noGEN.end.gendel	percent
uq reads:	1049656	322245	30.7001%
   reads: 	1157519	353649	30.5523%
----------------
Candidate breakpoint sites in file: EG40N_depletion.xls
  reads:	20658
  uqreads:	20427
  Number of reads supporting candidate sites:	20427

Level 1 collapse of depletion sites in file: EG40N_depletion_level1.xls
  Number of Level 1 collapsed sites:	2067