Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-383.fastq.uq.polyn	RAL-383.filter	percent
uq reads:	35630702	3850875	10.8077%
   reads: 	39125808	4757230	12.1588%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-383.filter	RAL-383.nostrna	percent
uq reads:	3850875	2072425	53.8170%
   reads: 	4757230	2604298	54.7440%
----------------
TE_filter:
  reads:	RAL-383.nostrna	RAL-383.noTE	percent
uq reads:	2072425	2058682	99.3369%
   reads: 	2604298	2586869	99.3308%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-383.noGEN.front	RAL-383.noGEN.front.gen	percent
uq reads:	2058682	652760	31.7077%
   reads: 	2586869	840151	32.4775%
----------------
match_TE:2:
  reads:	RAL-383.noGEN.front	RAL-383.noGEN.front.TE	percent
uq reads:	2058682	96966	4.7101%
   reads: 	2586869	108090	4.1784%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-383.noGEN.end	RAL-383.noGEN.end.gen	percent
uq reads:	2058682	559478	27.1765%
   reads: 	2586869	737665	28.5157%
----------------
match_TE:2:
  reads:	RAL-383.noGEN.end	RAL-383.noGEN.end.TE	percent
uq reads:	2058682	90357	4.3891%
   reads: 	2586869	102584	3.9656%
----------------
Candidate insertion sites in file: RAL-383_insert.txt
  reads:	14159
  uqreads:	13674
  Number of Candidate sites:	13674

Level 1 collapse of insertion sites in file: RAL-383_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	561

Level 1 annotation file: RAL-383_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-383_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-383.noGEN.front	RAL-383.noGEN.front.gendel	percent
uq reads:	2058682	664739	32.2895%
   reads: 	2586869	857255	33.1387%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-383.noGEN.end	RAL-383.noGEN.end.gendel	percent
uq reads:	2058682	568564	27.6179%
   reads: 	2586869	751494	29.0503%
----------------
Candidate breakpoint sites in file: RAL-383_depletion.xls
  reads:	34861
  uqreads:	33647
  Number of reads supporting candidate sites:	33647

Level 1 collapse of depletion sites in file: RAL-383_depletion_level1.xls
  Number of Level 1 collapsed sites:	2884