Insertion Pipeline Bowtie2_wholegenome: reads: W2.fastq.uq.polyn W2.filter percent uq reads: 50093650 1885951 3.7649% reads: 60461980 2874762 4.7547% ---------------- virus_structural_rna_repbase_filter: reads: W2.filter W2.nostrna percent uq reads: 1885951 1836023 97.3526% reads: 2874762 2781162 96.7441% ---------------- TE_filter: reads: W2.nostrna W2.noTE percent uq reads: 1836023 1830933 99.7228% reads: 2781162 2775409 99.7931% ---------------- match_dm6_mask_gen:1: reads: W2.noGEN.front W2.noGEN.front.gen percent uq reads: 1830933 601049 32.8275% reads: 2775409 1045125 37.6566% ---------------- match_TE:2: reads: W2.noGEN.front W2.noGEN.front.TE percent uq reads: 1830933 101803 5.5602% reads: 2775409 114481 4.1248% ---------------- match_dm6_mask_gen:1: reads: W2.noGEN.end W2.noGEN.end.gen percent uq reads: 1830933 640161 34.9636% reads: 2775409 1131596 40.7722% ---------------- match_TE:2: reads: W2.noGEN.end W2.noGEN.end.TE percent uq reads: 1830933 104101 5.6857% reads: 2775409 116045 4.1812% ---------------- Candidate insertion sites in file: W2_insert.txt reads: 27905 uqreads: 26145 Number of Candidate sites: 26145 Level 1 collapse of insertion sites in file: W2_insert_base22_W300_level1.xls Number of Level 1 collapsed sites: 1514 Level 1 annotation file: W2_level1siteannotation.xls Insertion sites in fixed bin: W2_insert_fixed_bin_5000.txt End of pipeline Beginning of Depletion Pipeline match_dm6_mask_gen_del:1: reads: W2.noGEN.front W2.noGEN.front.gendel percent uq reads: 1830933 601049 32.8275% reads: 2775409 1045125 37.6566% ---------------- match_dm6_mask_gen_del:1: reads: W2.noGEN.end W2.noGEN.end.gendel percent uq reads: 1830933 640161 34.9636% reads: 2775409 1131596 40.7722% ---------------- Candidate breakpoint sites in file: W2_depletion.xls reads: 36676 uqreads: 33766 Number of reads supporting candidate sites: 33766 Level 1 collapse of depletion sites in file: W2_depletion_level1.xls Number of Level 1 collapsed sites: 3023