Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-377.fastq.uq.polyn	RAL-377.filter	percent
uq reads:	39844850	3481963	8.7388%
   reads: 	43066729	4258230	9.8875%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-377.filter	RAL-377.nostrna	percent
uq reads:	3481963	3317514	95.2771%
   reads: 	4258230	3859740	90.6419%
----------------
TE_filter:
  reads:	RAL-377.nostrna	RAL-377.noTE	percent
uq reads:	3317514	3299550	99.4585%
   reads: 	3859740	3837417	99.4216%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-377.noGEN.front	RAL-377.noGEN.front.gen	percent
uq reads:	3299550	1118903	33.9108%
   reads: 	3837417	1233967	32.1562%
----------------
match_TE:2:
  reads:	RAL-377.noGEN.front	RAL-377.noGEN.front.TE	percent
uq reads:	3299550	175481	5.3183%
   reads: 	3837417	190118	4.9543%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-377.noGEN.end	RAL-377.noGEN.end.gen	percent
uq reads:	3299550	645439	19.5614%
   reads: 	3837417	751970	19.5957%
----------------
match_TE:2:
  reads:	RAL-377.noGEN.end	RAL-377.noGEN.end.TE	percent
uq reads:	3299550	124013	3.7585%
   reads: 	3837417	138983	3.6218%
----------------
Candidate insertion sites in file: RAL-377_insert.txt
  reads:	17247
  uqreads:	16836
  Number of Candidate sites:	16836

Level 1 collapse of insertion sites in file: RAL-377_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	765

Level 1 annotation file: RAL-377_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-377_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-377.noGEN.front	RAL-377.noGEN.front.gendel	percent
uq reads:	3299550	1139650	34.5396%
   reads: 	3837417	1257783	32.7768%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-377.noGEN.end	RAL-377.noGEN.end.gendel	percent
uq reads:	3299550	657730	19.9339%
   reads: 	3837417	766936	19.9857%
----------------
Candidate breakpoint sites in file: RAL-377_depletion.xls
  reads:	40823
  uqreads:	39769
  Number of reads supporting candidate sites:	39769

Level 1 collapse of depletion sites in file: RAL-377_depletion_level1.xls
  Number of Level 1 collapsed sites:	3467