{ "report_data_sources": { "RSeQC": { "infer_experiment": { "G176_M3_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/Read_Strandness/G176_M3_Read_Strandness.txt", "G176_M13_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/Read_Strandness/G176_M13_Read_Strandness.txt", "G176_M5_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/Read_Strandness/G176_M5_Read_Strandness.txt", "G176_M1_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/Read_Strandness/G176_M1_Read_Strandness.txt", "G176_M10_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/Read_Strandness/G176_M10_Read_Strandness.txt", "G176_M7_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/Read_Strandness/G176_M7_Read_Strandness.txt", "G176_M9_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/Read_Strandness/G176_M9_Read_Strandness.txt", "G176_M11_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/Read_Strandness/G176_M11_Read_Strandness.txt", "G176_M4_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/Read_Strandness/G176_M4_Read_Strandness.txt", "G176_M6_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/Read_Strandness/G176_M6_Read_Strandness.txt", "G176_M12_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/Read_Strandness/G176_M12_Read_Strandness.txt", "G176_M2_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/Read_Strandness/G176_M2_Read_Strandness.txt", "G176_M8_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/Read_Strandness/G176_M8_Read_Strandness.txt" } }, "featureCounts": { "all_sections": { "G176_M3_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M3_featureCounts.out.summary", "G176_M13_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M13_featureCounts.out.summary", "G176_M5_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M5_featureCounts.out.summary", "G176_M1_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M1_featureCounts.out.summary", "G176_M10_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M10_featureCounts.out.summary", "G176_M7_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M7_featureCounts.out.summary", "G176_M9_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M9_featureCounts.out.summary", "G176_M11_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M11_featureCounts.out.summary", "G176_M4_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M4_featureCounts.out.summary", "G176_M6_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M6_featureCounts.out.summary", "G176_M12_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M12_featureCounts.out.summary", "G176_M2_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M2_featureCounts.out.summary", "G176_M8_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G176_M8_featureCounts.out.summary" } }, "Samtools": { "flagstat": { "G176_M3_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/aligner/G176_M3_statistics_for_all_accepted_reads.txt", "G176_M3_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/aligner/G176_M3_statistics_for_primary_reads.txt", "G176_M3_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/aligner/G176_M3_statistics_for_primary_unique_reads.txt", "G176_M13_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/aligner/G176_M13_statistics_for_primary_unique_reads.txt", "G176_M13_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/aligner/G176_M13_statistics_for_all_accepted_reads.txt", "G176_M13_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/aligner/G176_M13_statistics_for_primary_reads.txt", "G176_M5_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/aligner/G176_M5_statistics_for_all_accepted_reads.txt", "G176_M5_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/aligner/G176_M5_statistics_for_primary_unique_reads.txt", "G176_M5_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/aligner/G176_M5_statistics_for_primary_reads.txt", "G176_M1_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/aligner/G176_M1_statistics_for_primary_reads.txt", "G176_M1_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/aligner/G176_M1_statistics_for_primary_unique_reads.txt", "G176_M1_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/aligner/G176_M1_statistics_for_all_accepted_reads.txt", "G176_M10_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/aligner/G176_M10_statistics_for_primary_unique_reads.txt", "G176_M10_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/aligner/G176_M10_statistics_for_all_accepted_reads.txt", "G176_M10_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/aligner/G176_M10_statistics_for_primary_reads.txt", "G176_M7_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/aligner/G176_M7_statistics_for_primary_reads.txt", "G176_M7_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/aligner/G176_M7_statistics_for_primary_unique_reads.txt", "G176_M7_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/aligner/G176_M7_statistics_for_all_accepted_reads.txt", "G176_M9_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/aligner/G176_M9_statistics_for_all_accepted_reads.txt", "G176_M9_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/aligner/G176_M9_statistics_for_primary_reads.txt", "G176_M9_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/aligner/G176_M9_statistics_for_primary_unique_reads.txt", "G176_M11_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/aligner/G176_M11_statistics_for_all_accepted_reads.txt", "G176_M11_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/aligner/G176_M11_statistics_for_primary_unique_reads.txt", "G176_M11_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/aligner/G176_M11_statistics_for_primary_reads.txt", "G176_M4_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/aligner/G176_M4_statistics_for_primary_unique_reads.txt", "G176_M4_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/aligner/G176_M4_statistics_for_all_accepted_reads.txt", "G176_M4_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/aligner/G176_M4_statistics_for_primary_reads.txt", "G176_M6_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/aligner/G176_M6_statistics_for_all_accepted_reads.txt", "G176_M6_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/aligner/G176_M6_statistics_for_primary_reads.txt", "G176_M6_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/aligner/G176_M6_statistics_for_primary_unique_reads.txt", "G176_M12_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/aligner/G176_M12_statistics_for_primary_unique_reads.txt", "G176_M12_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/aligner/G176_M12_statistics_for_all_accepted_reads.txt", "G176_M12_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/aligner/G176_M12_statistics_for_primary_reads.txt", "G176_M2_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/aligner/G176_M2_statistics_for_primary_reads.txt", "G176_M2_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/aligner/G176_M2_statistics_for_primary_unique_reads.txt", "G176_M2_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/aligner/G176_M2_statistics_for_all_accepted_reads.txt", "G176_M8_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/aligner/G176_M8_statistics_for_primary_reads.txt", "G176_M8_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/aligner/G176_M8_statistics_for_all_accepted_reads.txt", "G176_M8_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/aligner/G176_M8_statistics_for_primary_unique_reads.txt" } }, "STAR": { "SummaryLog": { "G176_M3_G176_M3": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M3/aligner/G176_M3_G176_M3_Log.final.out", "G176_M13_G176_M13": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M13/aligner/G176_M13_G176_M13_Log.final.out", "G176_M5_G176_M5": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M5/aligner/G176_M5_G176_M5_Log.final.out", "G176_M1_G176_M1": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M1/aligner/G176_M1_G176_M1_Log.final.out", "G176_M10_G176_M10": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M10/aligner/G176_M10_G176_M10_Log.final.out", "G176_M7_G176_M7": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M7/aligner/G176_M7_G176_M7_Log.final.out", "G176_M9_G176_M9": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M9/aligner/G176_M9_G176_M9_Log.final.out", "G176_M11_G176_M11": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M11/aligner/G176_M11_G176_M11_Log.final.out", "G176_M4_G176_M4": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M4/aligner/G176_M4_G176_M4_Log.final.out", "G176_M6_G176_M6": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M6/aligner/G176_M6_G176_M6_Log.final.out", "G176_M12_G176_M12": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M12/aligner/G176_M12_G176_M12_Log.final.out", "G176_M2_G176_M2": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M2/aligner/G176_M2_G176_M2_Log.final.out", "G176_M8_G176_M8": "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES/G176_M8/aligner/G176_M8_G176_M8_Log.final.out" } } }, "report_general_stats_data": [ { "G176_M3_sorted": { "Total": 11716153, "Assigned": 11205772, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 510381, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.64378341593867 }, "G176_M13_sorted": { "Total": 13652168, "Assigned": 12999508, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 652660, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.21936735615911 }, "G176_M5_sorted": { "Total": 21147704, "Assigned": 20320482, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 827222, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 96.08836023050067 }, "G176_M1_sorted": { "Total": 14115350, "Assigned": 13456245, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 659105, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.3305798297598 }, "G176_M10_sorted": { "Total": 12748631, "Assigned": 12061081, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 687550, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.60687190648157 }, "G176_M7_sorted": { "Total": 21751896, "Assigned": 20796741, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 955155, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.60886554441048 }, "G176_M9_sorted": { "Total": 9468579, "Assigned": 9067782, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 400797, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.76708395209039 }, "G176_M11_sorted": { "Total": 15205005, "Assigned": 14302966, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 902039, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.06748633098114 }, "G176_M4_sorted": { "Total": 15116811, "Assigned": 14541733, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 575078, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 96.1957717140209 }, "G176_M6_sorted": { "Total": 11736874, "Assigned": 11243142, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 493732, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.79332622979508 }, "G176_M12_sorted": { "Total": 14910642, "Assigned": 14262056, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 648586, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.65018058913896 }, "G176_M2_sorted": { "Total": 15301829, "Assigned": 14624479, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 677350, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.57340498315594 }, "G176_M8_sorted": { "Total": 16941303, "Assigned": 16212871, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 728432, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.70025989146171 } }, { "G176_M3_statistics_for_all_accepted_reads": { "total_passed": 26745316, "total_failed": 0, "secondary_passed": 2192908, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 26745316, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24552408, "paired in sequencing_failed": 0, "read1_passed": 12276204, "read1_failed": 0, "read2_passed": 12276204, "read2_failed": 0, "properly paired_passed": 24552408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24552408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 26745316 }, "G176_M3_statistics_for_primary_reads": { "total_passed": 24552408, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 24552408, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24552408, "paired in sequencing_failed": 0, "read1_passed": 12276204, "read1_failed": 0, "read2_passed": 12276204, "read2_failed": 0, "properly paired_passed": 24552408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24552408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 24552408 }, "G176_M3_statistics_for_primary_unique_reads": { "total_passed": 23432306, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 23432306, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 23432306, "paired in sequencing_failed": 0, "read1_passed": 11716153, "read1_failed": 0, "read2_passed": 11716153, "read2_failed": 0, "properly paired_passed": 23432306, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 23432306, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 23432306 }, "G176_M13_statistics_for_primary_unique_reads": { "total_passed": 27304336, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 27304336, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 27304336, "paired in sequencing_failed": 0, "read1_passed": 13652168, "read1_failed": 0, "read2_passed": 13652168, "read2_failed": 0, "properly paired_passed": 27304336, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 27304336, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 27304336 }, "G176_M13_statistics_for_all_accepted_reads": { "total_passed": 30735024, "total_failed": 0, "secondary_passed": 2217350, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30735024, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28517674, "paired in sequencing_failed": 0, "read1_passed": 14258837, "read1_failed": 0, "read2_passed": 14258837, "read2_failed": 0, "properly paired_passed": 28517674, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28517674, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30735024 }, "G176_M13_statistics_for_primary_reads": { "total_passed": 28517674, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 28517674, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28517674, "paired in sequencing_failed": 0, "read1_passed": 14258837, "read1_failed": 0, "read2_passed": 14258837, "read2_failed": 0, "properly paired_passed": 28517674, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28517674, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 28517674 }, "G176_M5_statistics_for_all_accepted_reads": { "total_passed": 49228966, "total_failed": 0, "secondary_passed": 4625282, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 49228966, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44603684, "paired in sequencing_failed": 0, "read1_passed": 22301842, "read1_failed": 0, "read2_passed": 22301842, "read2_failed": 0, "properly paired_passed": 44603684, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44603684, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 49228966 }, "G176_M5_statistics_for_primary_unique_reads": { "total_passed": 42295408, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 42295408, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 42295408, "paired in sequencing_failed": 0, "read1_passed": 21147704, "read1_failed": 0, "read2_passed": 21147704, "read2_failed": 0, "properly paired_passed": 42295408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 42295408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 42295408 }, "G176_M5_statistics_for_primary_reads": { "total_passed": 44603684, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 44603684, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44603684, "paired in sequencing_failed": 0, "read1_passed": 22301842, "read1_failed": 0, "read2_passed": 22301842, "read2_failed": 0, "properly paired_passed": 44603684, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44603684, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 44603684 }, "G176_M1_statistics_for_primary_reads": { "total_passed": 29796228, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29796228, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29796228, "paired in sequencing_failed": 0, "read1_passed": 14898114, "read1_failed": 0, "read2_passed": 14898114, "read2_failed": 0, "properly paired_passed": 29796228, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29796228, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29796228 }, "G176_M1_statistics_for_primary_unique_reads": { "total_passed": 28230700, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 28230700, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28230700, "paired in sequencing_failed": 0, "read1_passed": 14115350, "read1_failed": 0, "read2_passed": 14115350, "read2_failed": 0, "properly paired_passed": 28230700, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28230700, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 28230700 }, "G176_M1_statistics_for_all_accepted_reads": { "total_passed": 33223248, "total_failed": 0, "secondary_passed": 3427020, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33223248, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29796228, "paired in sequencing_failed": 0, "read1_passed": 14898114, "read1_failed": 0, "read2_passed": 14898114, "read2_failed": 0, "properly paired_passed": 29796228, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29796228, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33223248 }, "G176_M10_statistics_for_primary_unique_reads": { "total_passed": 25497262, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 25497262, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 25497262, "paired in sequencing_failed": 0, "read1_passed": 12748631, "read1_failed": 0, "read2_passed": 12748631, "read2_failed": 0, "properly paired_passed": 25497262, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 25497262, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 25497262 }, "G176_M10_statistics_for_all_accepted_reads": { "total_passed": 29087694, "total_failed": 0, "secondary_passed": 2242278, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29087694, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 26845416, "paired in sequencing_failed": 0, "read1_passed": 13422708, "read1_failed": 0, "read2_passed": 13422708, "read2_failed": 0, "properly paired_passed": 26845416, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 26845416, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29087694 }, "G176_M10_statistics_for_primary_reads": { "total_passed": 26845416, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 26845416, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 26845416, "paired in sequencing_failed": 0, "read1_passed": 13422708, "read1_failed": 0, "read2_passed": 13422708, "read2_failed": 0, "properly paired_passed": 26845416, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 26845416, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 26845416 }, "G176_M7_statistics_for_primary_reads": { "total_passed": 44990332, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 44990332, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44990332, "paired in sequencing_failed": 0, "read1_passed": 22495166, "read1_failed": 0, "read2_passed": 22495166, "read2_failed": 0, "properly paired_passed": 44990332, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44990332, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 44990332 }, "G176_M7_statistics_for_primary_unique_reads": { "total_passed": 43503792, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 43503792, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 43503792, "paired in sequencing_failed": 0, "read1_passed": 21751896, "read1_failed": 0, "read2_passed": 21751896, "read2_failed": 0, "properly paired_passed": 43503792, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 43503792, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 43503792 }, "G176_M7_statistics_for_all_accepted_reads": { "total_passed": 47588730, "total_failed": 0, "secondary_passed": 2598398, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 47588730, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44990332, "paired in sequencing_failed": 0, "read1_passed": 22495166, "read1_failed": 0, "read2_passed": 22495166, "read2_failed": 0, "properly paired_passed": 44990332, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44990332, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 47588730 }, "G176_M9_statistics_for_all_accepted_reads": { "total_passed": 21594844, "total_failed": 0, "secondary_passed": 1762472, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 21594844, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 19832372, "paired in sequencing_failed": 0, "read1_passed": 9916186, "read1_failed": 0, "read2_passed": 9916186, "read2_failed": 0, "properly paired_passed": 19832372, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 19832372, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 21594844 }, "G176_M9_statistics_for_primary_reads": { "total_passed": 19832372, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 19832372, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 19832372, "paired in sequencing_failed": 0, "read1_passed": 9916186, "read1_failed": 0, "read2_passed": 9916186, "read2_failed": 0, "properly paired_passed": 19832372, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 19832372, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 19832372 }, "G176_M9_statistics_for_primary_unique_reads": { "total_passed": 18937158, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 18937158, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 18937158, "paired in sequencing_failed": 0, "read1_passed": 9468579, "read1_failed": 0, "read2_passed": 9468579, "read2_failed": 0, "properly paired_passed": 18937158, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 18937158, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 18937158 }, "G176_M11_statistics_for_all_accepted_reads": { "total_passed": 34735060, "total_failed": 0, "secondary_passed": 2661790, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 34735060, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32073270, "paired in sequencing_failed": 0, "read1_passed": 16036635, "read1_failed": 0, "read2_passed": 16036635, "read2_failed": 0, "properly paired_passed": 32073270, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32073270, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 34735060 }, "G176_M11_statistics_for_primary_unique_reads": { "total_passed": 30410010, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30410010, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30410010, "paired in sequencing_failed": 0, "read1_passed": 15205005, "read1_failed": 0, "read2_passed": 15205005, "read2_failed": 0, "properly paired_passed": 30410010, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30410010, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30410010 }, "G176_M11_statistics_for_primary_reads": { "total_passed": 32073270, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 32073270, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32073270, "paired in sequencing_failed": 0, "read1_passed": 16036635, "read1_failed": 0, "read2_passed": 16036635, "read2_failed": 0, "properly paired_passed": 32073270, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32073270, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 32073270 }, "G176_M4_statistics_for_primary_unique_reads": { "total_passed": 30233622, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30233622, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30233622, "paired in sequencing_failed": 0, "read1_passed": 15116811, "read1_failed": 0, "read2_passed": 15116811, "read2_failed": 0, "properly paired_passed": 30233622, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30233622, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30233622 }, "G176_M4_statistics_for_all_accepted_reads": { "total_passed": 35553958, "total_failed": 0, "secondary_passed": 3648720, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35553958, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31905238, "paired in sequencing_failed": 0, "read1_passed": 15952619, "read1_failed": 0, "read2_passed": 15952619, "read2_failed": 0, "properly paired_passed": 31905238, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31905238, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35553958 }, "G176_M4_statistics_for_primary_reads": { "total_passed": 31905238, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 31905238, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31905238, "paired in sequencing_failed": 0, "read1_passed": 15952619, "read1_failed": 0, "read2_passed": 15952619, "read2_failed": 0, "properly paired_passed": 31905238, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31905238, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 31905238 }, "G176_M6_statistics_for_all_accepted_reads": { "total_passed": 27101554, "total_failed": 0, "secondary_passed": 2409650, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 27101554, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24691904, "paired in sequencing_failed": 0, "read1_passed": 12345952, "read1_failed": 0, "read2_passed": 12345952, "read2_failed": 0, "properly paired_passed": 24691904, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24691904, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 27101554 }, "G176_M6_statistics_for_primary_reads": { "total_passed": 24691904, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 24691904, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24691904, "paired in sequencing_failed": 0, "read1_passed": 12345952, "read1_failed": 0, "read2_passed": 12345952, "read2_failed": 0, "properly paired_passed": 24691904, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24691904, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 24691904 }, "G176_M6_statistics_for_primary_unique_reads": { "total_passed": 23473748, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 23473748, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 23473748, "paired in sequencing_failed": 0, "read1_passed": 11736874, "read1_failed": 0, "read2_passed": 11736874, "read2_failed": 0, "properly paired_passed": 23473748, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 23473748, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 23473748 }, "G176_M12_statistics_for_primary_unique_reads": { "total_passed": 29821284, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29821284, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29821284, "paired in sequencing_failed": 0, "read1_passed": 14910642, "read1_failed": 0, "read2_passed": 14910642, "read2_failed": 0, "properly paired_passed": 29821284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29821284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29821284 }, "G176_M12_statistics_for_all_accepted_reads": { "total_passed": 33615768, "total_failed": 0, "secondary_passed": 2441484, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33615768, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31174284, "paired in sequencing_failed": 0, "read1_passed": 15587142, "read1_failed": 0, "read2_passed": 15587142, "read2_failed": 0, "properly paired_passed": 31174284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31174284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33615768 }, "G176_M12_statistics_for_primary_reads": { "total_passed": 31174284, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 31174284, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31174284, "paired in sequencing_failed": 0, "read1_passed": 15587142, "read1_failed": 0, "read2_passed": 15587142, "read2_failed": 0, "properly paired_passed": 31174284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31174284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 31174284 }, "G176_M2_statistics_for_primary_reads": { "total_passed": 32276450, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 32276450, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32276450, "paired in sequencing_failed": 0, "read1_passed": 16138225, "read1_failed": 0, "read2_passed": 16138225, "read2_failed": 0, "properly paired_passed": 32276450, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32276450, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 32276450 }, "G176_M2_statistics_for_primary_unique_reads": { "total_passed": 30603658, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30603658, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30603658, "paired in sequencing_failed": 0, "read1_passed": 15301829, "read1_failed": 0, "read2_passed": 15301829, "read2_failed": 0, "properly paired_passed": 30603658, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30603658, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30603658 }, "G176_M2_statistics_for_all_accepted_reads": { "total_passed": 35834388, "total_failed": 0, "secondary_passed": 3557938, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35834388, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32276450, "paired in sequencing_failed": 0, "read1_passed": 16138225, "read1_failed": 0, "read2_passed": 16138225, "read2_failed": 0, "properly paired_passed": 32276450, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32276450, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35834388 }, "G176_M8_statistics_for_primary_reads": { "total_passed": 35283240, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35283240, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 35283240, "paired in sequencing_failed": 0, "read1_passed": 17641620, "read1_failed": 0, "read2_passed": 17641620, "read2_failed": 0, "properly paired_passed": 35283240, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 35283240, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35283240 }, "G176_M8_statistics_for_all_accepted_reads": { "total_passed": 37630380, "total_failed": 0, "secondary_passed": 2347140, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 37630380, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 35283240, "paired in sequencing_failed": 0, "read1_passed": 17641620, "read1_failed": 0, "read2_passed": 17641620, "read2_failed": 0, "properly paired_passed": 35283240, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 35283240, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 37630380 }, "G176_M8_statistics_for_primary_unique_reads": { "total_passed": 33882606, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33882606, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 33882606, "paired in sequencing_failed": 0, "read1_passed": 16941303, "read1_failed": 0, "read2_passed": 16941303, "read2_failed": 0, "properly paired_passed": 33882606, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 33882606, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33882606 } }, { "G176_M3_G176_M3": { "total_reads": 15369699.0, "avg_input_read_length": 300.0, "uniquely_mapped": 11716153.0, "uniquely_mapped_percent": 76.23, "avg_mapped_read_length": 286.74, "num_splices": 12660512.0, "num_annotated_splices": 12277600.0, "num_GTAG_splices": 12587323.0, "num_GCAG_splices": 61742.0, "num_ATAC_splices": 3892.0, "num_noncanonical_splices": 7555.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.28, "insertion_rate": 0.01, "insertion_length": 1.97, "multimapped": 560051.0, "multimapped_percent": 3.64, "multimapped_toomany": 34615.0, "multimapped_toomany_percent": 0.23, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 17.38, "unmapped_other_percent": 2.52, "unmapped_mismatches": 0, "unmapped_tooshort": 2671524, "unmapped_other": 387356 }, "G176_M13_G176_M13": { "total_reads": 16992425.0, "avg_input_read_length": 300.0, "uniquely_mapped": 13652168.0, "uniquely_mapped_percent": 80.34, "avg_mapped_read_length": 290.03, "num_splices": 13204101.0, "num_annotated_splices": 12743935.0, "num_GTAG_splices": 13115677.0, "num_GCAG_splices": 74092.0, "num_ATAC_splices": 4985.0, "num_noncanonical_splices": 9347.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.37, "insertion_rate": 0.02, "insertion_length": 2.06, "multimapped": 606669.0, "multimapped_percent": 3.57, "multimapped_toomany": 33906.0, "multimapped_toomany_percent": 0.2, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.8, "unmapped_other_percent": 2.09, "unmapped_mismatches": 0, "unmapped_tooshort": 2344595, "unmapped_other": 355087 }, "G176_M5_G176_M5": { "total_reads": 27035045.0, "avg_input_read_length": 300.0, "uniquely_mapped": 21147704.0, "uniquely_mapped_percent": 78.22, "avg_mapped_read_length": 289.67, "num_splices": 24164544.0, "num_annotated_splices": 23414703.0, "num_GTAG_splices": 24010075.0, "num_GCAG_splices": 131284.0, "num_ATAC_splices": 8267.0, "num_noncanonical_splices": 14918.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.25, "insertion_rate": 0.01, "insertion_length": 1.96, "multimapped": 1154138.0, "multimapped_percent": 4.27, "multimapped_toomany": 71979.0, "multimapped_toomany_percent": 0.27, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.19, "unmapped_other_percent": 4.05, "unmapped_mismatches": 0, "unmapped_tooshort": 3566215, "unmapped_other": 1095009 }, "G176_M1_G176_M1": { "total_reads": 19736008.0, "avg_input_read_length": 300.0, "uniquely_mapped": 14115350.0, "uniquely_mapped_percent": 71.52, "avg_mapped_read_length": 288.01, "num_splices": 14736469.0, "num_annotated_splices": 14278719.0, "num_GTAG_splices": 14647634.0, "num_GCAG_splices": 75668.0, "num_ATAC_splices": 4850.0, "num_noncanonical_splices": 8317.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.3, "insertion_rate": 0.01, "insertion_length": 1.96, "multimapped": 782764.0, "multimapped_percent": 3.97, "multimapped_toomany": 59441.0, "multimapped_toomany_percent": 0.3, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 16.77, "unmapped_other_percent": 7.44, "unmapped_mismatches": 0, "unmapped_tooshort": 3309982, "unmapped_other": 1468471 }, "G176_M10_G176_M10": { "total_reads": 16436531.0, "avg_input_read_length": 300.0, "uniquely_mapped": 12748631.0, "uniquely_mapped_percent": 77.56, "avg_mapped_read_length": 288.23, "num_splices": 13323078.0, "num_annotated_splices": 12906333.0, "num_GTAG_splices": 13240762.0, "num_GCAG_splices": 70318.0, "num_ATAC_splices": 4171.0, "num_noncanonical_splices": 7827.0, "mismatch_rate": 0.27, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 1.92, "multimapped": 674077.0, "multimapped_percent": 4.1, "multimapped_toomany": 26900.0, "multimapped_toomany_percent": 0.16, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 15.92, "unmapped_other_percent": 2.26, "unmapped_mismatches": 0, "unmapped_tooshort": 2615611, "unmapped_other": 371312 }, "G176_M7_G176_M7": { "total_reads": 27617494.0, "avg_input_read_length": 300.0, "uniquely_mapped": 21751896.0, "uniquely_mapped_percent": 78.76, "avg_mapped_read_length": 288.52, "num_splices": 19155883.0, "num_annotated_splices": 18567393.0, "num_GTAG_splices": 19065610.0, "num_GCAG_splices": 74230.0, "num_ATAC_splices": 4475.0, "num_noncanonical_splices": 11568.0, "mismatch_rate": 0.32, "deletion_rate": 0.02, "deletion_length": 2.45, "insertion_rate": 0.02, "insertion_length": 2.04, "multimapped": 743270.0, "multimapped_percent": 2.69, "multimapped_toomany": 39409.0, "multimapped_toomany_percent": 0.14, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 17.6, "unmapped_other_percent": 0.81, "unmapped_mismatches": 0, "unmapped_tooshort": 4859282, "unmapped_other": 223637 }, "G176_M9_G176_M9": { "total_reads": 12394901.0, "avg_input_read_length": 300.0, "uniquely_mapped": 9468579.0, "uniquely_mapped_percent": 76.39, "avg_mapped_read_length": 288.06, "num_splices": 10068199.0, "num_annotated_splices": 9773809.0, "num_GTAG_splices": 10007181.0, "num_GCAG_splices": 52449.0, "num_ATAC_splices": 3063.0, "num_noncanonical_splices": 5506.0, "mismatch_rate": 0.3, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 2.03, "multimapped": 447607.0, "multimapped_percent": 3.61, "multimapped_toomany": 26753.0, "multimapped_toomany_percent": 0.22, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 16.06, "unmapped_other_percent": 3.72, "unmapped_mismatches": 0, "unmapped_tooshort": 1990825, "unmapped_other": 461137 }, "G176_M11_G176_M11": { "total_reads": 19227077.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15205005.0, "uniquely_mapped_percent": 79.08, "avg_mapped_read_length": 288.63, "num_splices": 16290713.0, "num_annotated_splices": 15817966.0, "num_GTAG_splices": 16195720.0, "num_GCAG_splices": 79803.0, "num_ATAC_splices": 5078.0, "num_noncanonical_splices": 10112.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.55, "insertion_rate": 0.01, "insertion_length": 2.07, "multimapped": 831630.0, "multimapped_percent": 4.33, "multimapped_toomany": 24481.0, "multimapped_toomany_percent": 0.13, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 15.31, "unmapped_other_percent": 1.16, "unmapped_mismatches": 0, "unmapped_tooshort": 2942979, "unmapped_other": 222982 }, "G176_M4_G176_M4": { "total_reads": 20125707.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15116811.0, "uniquely_mapped_percent": 75.11, "avg_mapped_read_length": 288.98, "num_splices": 17152590.0, "num_annotated_splices": 16574210.0, "num_GTAG_splices": 17031562.0, "num_GCAG_splices": 103750.0, "num_ATAC_splices": 6831.0, "num_noncanonical_splices": 10447.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.25, "insertion_rate": 0.01, "insertion_length": 2.06, "multimapped": 835808.0, "multimapped_percent": 4.15, "multimapped_toomany": 66158.0, "multimapped_toomany_percent": 0.33, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.61, "unmapped_other_percent": 6.8, "unmapped_mismatches": 0, "unmapped_tooshort": 2738624, "unmapped_other": 1368306 }, "G176_M6_G176_M6": { "total_reads": 15118820.0, "avg_input_read_length": 300.0, "uniquely_mapped": 11736874.0, "uniquely_mapped_percent": 77.63, "avg_mapped_read_length": 290.16, "num_splices": 12754848.0, "num_annotated_splices": 12344596.0, "num_GTAG_splices": 12671392.0, "num_GCAG_splices": 70725.0, "num_ATAC_splices": 4739.0, "num_noncanonical_splices": 7992.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 2.04, "multimapped": 609078.0, "multimapped_percent": 4.03, "multimapped_toomany": 35430.0, "multimapped_toomany_percent": 0.23, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 12.71, "unmapped_other_percent": 5.39, "unmapped_mismatches": 0, "unmapped_tooshort": 1922256, "unmapped_other": 815182 }, "G176_M12_G176_M12": { "total_reads": 18558269.0, "avg_input_read_length": 300.0, "uniquely_mapped": 14910642.0, "uniquely_mapped_percent": 80.35, "avg_mapped_read_length": 289.07, "num_splices": 15462944.0, "num_annotated_splices": 14937250.0, "num_GTAG_splices": 15356604.0, "num_GCAG_splices": 90730.0, "num_ATAC_splices": 5476.0, "num_noncanonical_splices": 10134.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.28, "insertion_rate": 0.01, "insertion_length": 1.99, "multimapped": 676500.0, "multimapped_percent": 3.65, "multimapped_toomany": 31310.0, "multimapped_toomany_percent": 0.17, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 14.79, "unmapped_other_percent": 1.05, "unmapped_mismatches": 0, "unmapped_tooshort": 2744943, "unmapped_other": 194874 }, "G176_M2_G176_M2": { "total_reads": 20619409.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15301829.0, "uniquely_mapped_percent": 74.21, "avg_mapped_read_length": 288.43, "num_splices": 16105855.0, "num_annotated_splices": 15585021.0, "num_GTAG_splices": 16005484.0, "num_GCAG_splices": 86265.0, "num_ATAC_splices": 5334.0, "num_noncanonical_splices": 8772.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.39, "insertion_rate": 0.01, "insertion_length": 1.97, "multimapped": 836396.0, "multimapped_percent": 4.06, "multimapped_toomany": 62711.0, "multimapped_toomany_percent": 0.3, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 14.72, "unmapped_other_percent": 6.7, "unmapped_mismatches": 0, "unmapped_tooshort": 3036411, "unmapped_other": 1382062 }, "G176_M8_G176_M8": { "total_reads": 20671637.0, "avg_input_read_length": 300.0, "uniquely_mapped": 16941303.0, "uniquely_mapped_percent": 81.95, "avg_mapped_read_length": 289.87, "num_splices": 18467987.0, "num_annotated_splices": 17945904.0, "num_GTAG_splices": 18365300.0, "num_GCAG_splices": 87327.0, "num_ATAC_splices": 5212.0, "num_noncanonical_splices": 10148.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.36, "insertion_rate": 0.01, "insertion_length": 1.98, "multimapped": 700317.0, "multimapped_percent": 3.39, "multimapped_toomany": 28763.0, "multimapped_toomany_percent": 0.14, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.91, "unmapped_other_percent": 0.61, "unmapped_mismatches": 0, "unmapped_tooshort": 2875168, "unmapped_other": 126086 } } ], "report_general_stats_headers": [ { "percent_assigned": { "title": "% Assigned", "description": "% Assigned reads", "max": 100, "min": 0, "suffix": "%", "scale": "RdYlGn", "namespace": "featureCounts", "rid": "mqc-generalstats-featurecounts-percent_assigned", "format": "{:,.1f}", "colour": "55,126,184", "hidden": null, "ceiling": null, "floor": null, "minRange": null, "shared_key": null, "modify": null, "placement": 1000.0, "dmax": 100.0, "dmin": 0.0 }, "Assigned": { "title": "M Assigned", "description": "Assigned reads (millions)", "min": 0, "scale": "PuBu", "modify": 1e-06, "shared_key": "read_count", "namespace": "featureCounts", "rid": "mqc-generalstats-featurecounts-Assigned", "format": "{:,.1f}", "colour": "55,126,184", "hidden": null, "max": null, "ceiling": null, "floor": null, "minRange": null, "placement": 1000.0, "dmax": 49.228966, "dmin": 0.0 } }, { "flagstat_total": { "title": "M Reads", "description": "Total reads in the bam file (millions)", "min": 0, "modify": 1e-06, "shared_key": "read_count", "placement": 100.0, "hidden": true, "namespace": "Samtools", "rid": "mqc-generalstats-samtools-flagstat_total", "scale": "GnBu", "format": "{:,.1f}", "colour": "77,175,74", "max": null, "ceiling": null, "floor": null, "minRange": null, "dmax": 49.228966, "dmin": 0.0 }, "mapped_passed": { "title": "M Reads Mapped", "description": "Reads Mapped in the bam file (millions)", "min": 0, "modify": 1e-06, "shared_key": "read_count", "placement": 101.0, "namespace": "Samtools", "rid": "mqc-generalstats-samtools-mapped_passed", "scale": "GnBu", "format": "{:,.1f}", "colour": "77,175,74", "hidden": null, "max": null, "ceiling": null, "floor": null, "minRange": null, "dmax": 49.228966, "dmin": 0.0 } }, { "uniquely_mapped_percent": { "title": "% Aligned", "description": "% Uniquely mapped reads", "max": 100, "min": 0, "suffix": "%", "scale": "YlGn", "namespace": "STAR", "rid": "mqc-generalstats-star-uniquely_mapped_percent", "format": "{:,.1f}", "colour": "152,78,163", "hidden": null, "ceiling": null, "floor": null, "minRange": null, "shared_key": null, "modify": null, "placement": 1000.0, "dmax": 100.0, "dmin": 0.0 }, "uniquely_mapped": { "title": "M Aligned", "description": "Uniquely mapped reads (millions)", "min": 0, "scale": "PuRd", "modify": 1e-06, "shared_key": "read_count", "namespace": "STAR", "rid": "mqc-generalstats-star-uniquely_mapped", "format": "{:,.1f}", "colour": "152,78,163", "hidden": null, "max": null, "ceiling": null, "floor": null, "minRange": null, "placement": 1000.0, "dmax": 49.228966, "dmin": 0.0 } } ], "report_multiqc_command": "/projectnb/wax-es/routines/condaenv/multiqc/bin/multiqc --no-ansi -c /projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/14_final_summary/Scripts/multiqc_config.yaml /projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES /projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/03_FASTQC/ /projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/06_CollectMetrics/", "report_plot_data": { "rseqc_infer_experiment_plot": { "plot_type": "bar_graph", "samples": [ [ "G176_M10_Read_Strandness", "G176_M11_Read_Strandness", "G176_M12_Read_Strandness", "G176_M13_Read_Strandness", "G176_M1_Read_Strandness", "G176_M2_Read_Strandness", "G176_M3_Read_Strandness", "G176_M4_Read_Strandness", "G176_M5_Read_Strandness", "G176_M6_Read_Strandness", "G176_M7_Read_Strandness", "G176_M8_Read_Strandness", "G176_M9_Read_Strandness" ] ], "datasets": [ [ { "name": "Sense", "data": [ 1.05, 1.06, 1.09, 1.05, 1.17, 0.88, 0.8500000000000001, 0.8999999999999999, 0.8, 0.8699999999999999, 1.1400000000000001, 0.95, 0.88 ] }, { "name": "Antisense", "data": [ 96.98, 97.08, 96.78, 96.97, 96.63000000000001, 96.92, 97.05, 97.16, 97.13000000000001, 97.21, 97.05, 97.02, 97.28 ] }, { "name": "Undetermined", "data": [ 1.97, 1.8599999999999999, 2.13, 1.97, 2.19, 2.1999999999999997, 2.1, 1.94, 2.07, 1.92, 1.7999999999999998, 2.02, 1.8399999999999999 ] } ] ], "config": { "id": "rseqc_infer_experiment_plot", "title": "RSeQC: Infer experiment", "ylab": "% Tags", "ymin": 0, "ymax": 100, "tt_percentages": false, "ylab_format": "{value}%", "cpswitch": false } }, "featureCounts_assignment_plot": { "plot_type": "bar_graph", "samples": [ [ "G176_M10_sorted", "G176_M11_sorted", "G176_M12_sorted", "G176_M13_sorted", "G176_M1_sorted", "G176_M2_sorted", "G176_M3_sorted", "G176_M4_sorted", "G176_M5_sorted", "G176_M6_sorted", "G176_M7_sorted", "G176_M8_sorted", "G176_M9_sorted" ] ], "datasets": [ [ { "name": "Assigned", "data": [ 12061081.0, 14302966.0, 14262056.0, 12999508.0, 13456245.0, 14624479.0, 11205772.0, 14541733.0, 20320482.0, 11243142.0, 20796741.0, 16212871.0, 9067782.0 ] }, { "name": "Unassigned: No Features", "data": [ 687550.0, 902039.0, 648586.0, 652660.0, 659105.0, 677350.0, 510381.0, 575078.0, 827222.0, 493732.0, 955155.0, 728432.0, 400797.0 ] } ] ], "config": { "id": "featureCounts_assignment_plot", "title": "featureCounts: Assignments", "ylab": "# Reads", "cpswitch_counts_label": "Number of Reads" } }, "samtools-flagstat-dp": { "plot_type": "beeswarm", "samples": [ [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ], [ "G176_M3_statistics_for_all_accepted_reads", "G176_M3_statistics_for_primary_reads", "G176_M3_statistics_for_primary_unique_reads", "G176_M13_statistics_for_primary_unique_reads", "G176_M13_statistics_for_all_accepted_reads", "G176_M13_statistics_for_primary_reads", "G176_M5_statistics_for_all_accepted_reads", "G176_M5_statistics_for_primary_unique_reads", "G176_M5_statistics_for_primary_reads", "G176_M1_statistics_for_primary_reads", "G176_M1_statistics_for_primary_unique_reads", "G176_M1_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_unique_reads", "G176_M10_statistics_for_all_accepted_reads", "G176_M10_statistics_for_primary_reads", "G176_M7_statistics_for_primary_reads", "G176_M7_statistics_for_primary_unique_reads", "G176_M7_statistics_for_all_accepted_reads", "G176_M9_statistics_for_all_accepted_reads", "G176_M9_statistics_for_primary_reads", "G176_M9_statistics_for_primary_unique_reads", "G176_M11_statistics_for_all_accepted_reads", "G176_M11_statistics_for_primary_unique_reads", "G176_M11_statistics_for_primary_reads", "G176_M4_statistics_for_primary_unique_reads", "G176_M4_statistics_for_all_accepted_reads", "G176_M4_statistics_for_primary_reads", "G176_M6_statistics_for_all_accepted_reads", "G176_M6_statistics_for_primary_reads", "G176_M6_statistics_for_primary_unique_reads", "G176_M12_statistics_for_primary_unique_reads", "G176_M12_statistics_for_all_accepted_reads", "G176_M12_statistics_for_primary_reads", "G176_M2_statistics_for_primary_reads", "G176_M2_statistics_for_primary_unique_reads", "G176_M2_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_reads", "G176_M8_statistics_for_all_accepted_reads", "G176_M8_statistics_for_primary_unique_reads" ] ], "datasets": [ [ 26.745316, 24.552408, 23.432306, 27.304336, 30.735024, 28.517674, 49.228966, 42.295407999999995, 44.603684, 29.796228, 28.2307, 33.223248, 25.497262, 29.087694, 26.845416, 44.990331999999995, 43.503792, 47.58873, 21.594844, 19.832372, 18.937158, 34.73506, 30.41001, 32.07327, 30.233621999999997, 35.553958, 31.905237999999997, 27.101554, 24.691903999999997, 23.473748, 29.821284, 33.615767999999996, 31.174284, 32.27645, 30.603658, 35.834388, 35.28324, 37.630379999999995, 33.882605999999996 ], [ 26.745316, 24.552408, 23.432306, 27.304336, 30.735024, 28.517674, 49.228966, 42.295407999999995, 44.603684, 29.796228, 28.2307, 33.223248, 25.497262, 29.087694, 26.845416, 44.990331999999995, 43.503792, 47.58873, 21.594844, 19.832372, 18.937158, 34.73506, 30.41001, 32.07327, 30.233621999999997, 35.553958, 31.905237999999997, 27.101554, 24.691903999999997, 23.473748, 29.821284, 33.615767999999996, 31.174284, 32.27645, 30.603658, 35.834388, 35.28324, 37.630379999999995, 33.882605999999996 ], [ 26.745316, 24.552408, 23.432306, 27.304336, 30.735024, 28.517674, 49.228966, 42.295407999999995, 44.603684, 29.796228, 28.2307, 33.223248, 25.497262, 29.087694, 26.845416, 44.990331999999995, 43.503792, 47.58873, 21.594844, 19.832372, 18.937158, 34.73506, 30.41001, 32.07327, 30.233621999999997, 35.553958, 31.905237999999997, 27.101554, 24.691903999999997, 23.473748, 29.821284, 33.615767999999996, 31.174284, 32.27645, 30.603658, 35.834388, 35.28324, 37.630379999999995, 33.882605999999996 ], [ 2.192908, 0.0, 0.0, 0.0, 2.2173499999999997, 0.0, 4.6252819999999994, 0.0, 0.0, 0.0, 0.0, 3.4270199999999997, 0.0, 2.2422779999999998, 0.0, 0.0, 0.0, 2.598398, 1.7624719999999998, 0.0, 0.0, 2.66179, 0.0, 0.0, 0.0, 3.64872, 0.0, 2.40965, 0.0, 0.0, 0.0, 2.441484, 0.0, 0.0, 0.0, 3.557938, 0.0, 2.34714, 0.0 ], [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ], [ 24.552408, 24.552408, 23.432306, 27.304336, 28.517674, 28.517674, 44.603684, 42.295407999999995, 44.603684, 29.796228, 28.2307, 29.796228, 25.497262, 26.845416, 26.845416, 44.990331999999995, 43.503792, 44.990331999999995, 19.832372, 19.832372, 18.937158, 32.07327, 30.41001, 32.07327, 30.233621999999997, 31.905237999999997, 31.905237999999997, 24.691903999999997, 24.691903999999997, 23.473748, 29.821284, 31.174284, 31.174284, 32.27645, 30.603658, 32.27645, 35.28324, 35.28324, 33.882605999999996 ], [ 24.552408, 24.552408, 23.432306, 27.304336, 28.517674, 28.517674, 44.603684, 42.295407999999995, 44.603684, 29.796228, 28.2307, 29.796228, 25.497262, 26.845416, 26.845416, 44.990331999999995, 43.503792, 44.990331999999995, 19.832372, 19.832372, 18.937158, 32.07327, 30.41001, 32.07327, 30.233621999999997, 31.905237999999997, 31.905237999999997, 24.691903999999997, 24.691903999999997, 23.473748, 29.821284, 31.174284, 31.174284, 32.27645, 30.603658, 32.27645, 35.28324, 35.28324, 33.882605999999996 ], [ 24.552408, 24.552408, 23.432306, 27.304336, 28.517674, 28.517674, 44.603684, 42.295407999999995, 44.603684, 29.796228, 28.2307, 29.796228, 25.497262, 26.845416, 26.845416, 44.990331999999995, 43.503792, 44.990331999999995, 19.832372, 19.832372, 18.937158, 32.07327, 30.41001, 32.07327, 30.233621999999997, 31.905237999999997, 31.905237999999997, 24.691903999999997, 24.691903999999997, 23.473748, 29.821284, 31.174284, 31.174284, 32.27645, 30.603658, 32.27645, 35.28324, 35.28324, 33.882605999999996 ], [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ] ], "categories": [ { "namespace": "", "title": "Total Reads", "description": "Total Reads", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Total Passed QC", "description": "Total Passed QC", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Mapped", "description": "Mapped", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Secondary Alignments", "description": "Secondary Alignments", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Duplicates", "description": "Duplicates", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Paired in Sequencing", "description": "Paired in Sequencing", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Properly Paired", "description": "Properly Paired", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Self and mate mapped", "description": "Reads with itself and mate mapped", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Singletons", "description": "Singletons", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Mate mapped to diff chr", "description": "Mate mapped to different chromosome", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" }, { "namespace": "", "title": "Diff chr (mapQ >= 5)", "description": "Mate mapped to different chromosome (mapQ >= 5)", "max": 49.228966, "min": 0.0, "suffix": "M reads", "decimalPlaces": 2, "bordercol": "rgb(55,126,184)" } ] }, "star_alignment_plot": { "plot_type": "bar_graph", "samples": [ [ "G176_M10_G176_M10", "G176_M11_G176_M11", "G176_M12_G176_M12", "G176_M13_G176_M13", "G176_M1_G176_M1", "G176_M2_G176_M2", "G176_M3_G176_M3", "G176_M4_G176_M4", "G176_M5_G176_M5", "G176_M6_G176_M6", "G176_M7_G176_M7", "G176_M8_G176_M8", "G176_M9_G176_M9" ] ], "datasets": [ [ { "name": "Uniquely mapped", "data": [ 12748631.0, 15205005.0, 14910642.0, 13652168.0, 14115350.0, 15301829.0, 11716153.0, 15116811.0, 21147704.0, 11736874.0, 21751896.0, 16941303.0, 9468579.0 ], "color": "#437bb1" }, { "name": "Mapped to multiple loci", "data": [ 674077.0, 831630.0, 676500.0, 606669.0, 782764.0, 836396.0, 560051.0, 835808.0, 1154138.0, 609078.0, 743270.0, 700317.0, 447607.0 ], "color": "#7cb5ec" }, { "name": "Mapped to too many loci", "data": [ 26900.0, 24481.0, 31310.0, 33906.0, 59441.0, 62711.0, 34615.0, 66158.0, 71979.0, 35430.0, 39409.0, 28763.0, 26753.0 ], "color": "#f7a35c" }, { "name": "Unmapped: too short", "data": [ 2615611.0, 2942979.0, 2744943.0, 2344595.0, 3309982.0, 3036411.0, 2671524.0, 2738624.0, 3566215.0, 1922256.0, 4859282.0, 2875168.0, 1990825.0 ], "color": "#b1084c" }, { "name": "Unmapped: other", "data": [ 371312.0, 222982.0, 194874.0, 355087.0, 1468471.0, 1382062.0, 387356.0, 1368306.0, 1095009.0, 815182.0, 223637.0, 126086.0, 461137.0 ], "color": "#7f0000" } ] ], "config": { "id": "star_alignment_plot", "title": "STAR: Alignment Scores", "ylab": "# Reads", "cpswitch_counts_label": "Number of Reads" } } }, "report_saved_raw_data": { "multiqc_rseqc_infer_experiment": { "G176_M3_Read_Strandness": { "pe_sense": 0.0085, "pe_antisense": 0.9705, "failed": 0.021 }, "G176_M13_Read_Strandness": { "pe_sense": 0.0105, "pe_antisense": 0.9697, "failed": 0.0197 }, "G176_M5_Read_Strandness": { "pe_sense": 0.008, "pe_antisense": 0.9713, "failed": 0.0207 }, "G176_M1_Read_Strandness": { "pe_sense": 0.0117, "pe_antisense": 0.9663, "failed": 0.0219 }, "G176_M10_Read_Strandness": { "pe_sense": 0.0105, "pe_antisense": 0.9698, "failed": 0.0197 }, "G176_M7_Read_Strandness": { "pe_sense": 0.0114, "pe_antisense": 0.9705, "failed": 0.018 }, "G176_M9_Read_Strandness": { "pe_sense": 0.0088, "pe_antisense": 0.9728, "failed": 0.0184 }, "G176_M11_Read_Strandness": { "pe_sense": 0.0106, "pe_antisense": 0.9708, "failed": 0.0186 }, "G176_M4_Read_Strandness": { "pe_sense": 0.009, "pe_antisense": 0.9716, "failed": 0.0194 }, "G176_M6_Read_Strandness": { "pe_sense": 0.0087, "pe_antisense": 0.9721, "failed": 0.0192 }, "G176_M12_Read_Strandness": { "pe_sense": 0.0109, "pe_antisense": 0.9678, "failed": 0.0213 }, "G176_M2_Read_Strandness": { "pe_sense": 0.0088, "pe_antisense": 0.9692, "failed": 0.022 }, "G176_M8_Read_Strandness": { "pe_sense": 0.0095, "pe_antisense": 0.9702, "failed": 0.0202 } }, "multiqc_featureCounts": { "G176_M3_sorted": { "Total": 11716153, "Assigned": 11205772, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 510381, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.64378341593867 }, "G176_M13_sorted": { "Total": 13652168, "Assigned": 12999508, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 652660, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.21936735615911 }, "G176_M5_sorted": { "Total": 21147704, "Assigned": 20320482, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 827222, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 96.08836023050067 }, "G176_M1_sorted": { "Total": 14115350, "Assigned": 13456245, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 659105, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.3305798297598 }, "G176_M10_sorted": { "Total": 12748631, "Assigned": 12061081, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 687550, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.60687190648157 }, "G176_M7_sorted": { "Total": 21751896, "Assigned": 20796741, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 955155, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.60886554441048 }, "G176_M9_sorted": { "Total": 9468579, "Assigned": 9067782, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 400797, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.76708395209039 }, "G176_M11_sorted": { "Total": 15205005, "Assigned": 14302966, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 902039, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.06748633098114 }, "G176_M4_sorted": { "Total": 15116811, "Assigned": 14541733, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 575078, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 96.1957717140209 }, "G176_M6_sorted": { "Total": 11736874, "Assigned": 11243142, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 493732, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.79332622979508 }, "G176_M12_sorted": { "Total": 14910642, "Assigned": 14262056, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 648586, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.65018058913896 }, "G176_M2_sorted": { "Total": 15301829, "Assigned": 14624479, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 677350, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.57340498315594 }, "G176_M8_sorted": { "Total": 16941303, "Assigned": 16212871, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 728432, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.70025989146171 } }, "multiqc_samtools_flagstat": { "G176_M3_statistics_for_all_accepted_reads": { "total_passed": 26745316, "total_failed": 0, "secondary_passed": 2192908, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 26745316, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24552408, "paired in sequencing_failed": 0, "read1_passed": 12276204, "read1_failed": 0, "read2_passed": 12276204, "read2_failed": 0, "properly paired_passed": 24552408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24552408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 26745316 }, "G176_M3_statistics_for_primary_reads": { "total_passed": 24552408, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 24552408, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24552408, "paired in sequencing_failed": 0, "read1_passed": 12276204, "read1_failed": 0, "read2_passed": 12276204, "read2_failed": 0, "properly paired_passed": 24552408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24552408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 24552408 }, "G176_M3_statistics_for_primary_unique_reads": { "total_passed": 23432306, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 23432306, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 23432306, "paired in sequencing_failed": 0, "read1_passed": 11716153, "read1_failed": 0, "read2_passed": 11716153, "read2_failed": 0, "properly paired_passed": 23432306, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 23432306, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 23432306 }, "G176_M13_statistics_for_primary_unique_reads": { "total_passed": 27304336, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 27304336, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 27304336, "paired in sequencing_failed": 0, "read1_passed": 13652168, "read1_failed": 0, "read2_passed": 13652168, "read2_failed": 0, "properly paired_passed": 27304336, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 27304336, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 27304336 }, "G176_M13_statistics_for_all_accepted_reads": { "total_passed": 30735024, "total_failed": 0, "secondary_passed": 2217350, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30735024, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28517674, "paired in sequencing_failed": 0, "read1_passed": 14258837, "read1_failed": 0, "read2_passed": 14258837, "read2_failed": 0, "properly paired_passed": 28517674, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28517674, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30735024 }, "G176_M13_statistics_for_primary_reads": { "total_passed": 28517674, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 28517674, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28517674, "paired in sequencing_failed": 0, "read1_passed": 14258837, "read1_failed": 0, "read2_passed": 14258837, "read2_failed": 0, "properly paired_passed": 28517674, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28517674, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 28517674 }, "G176_M5_statistics_for_all_accepted_reads": { "total_passed": 49228966, "total_failed": 0, "secondary_passed": 4625282, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 49228966, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44603684, "paired in sequencing_failed": 0, "read1_passed": 22301842, "read1_failed": 0, "read2_passed": 22301842, "read2_failed": 0, "properly paired_passed": 44603684, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44603684, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 49228966 }, "G176_M5_statistics_for_primary_unique_reads": { "total_passed": 42295408, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 42295408, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 42295408, "paired in sequencing_failed": 0, "read1_passed": 21147704, "read1_failed": 0, "read2_passed": 21147704, "read2_failed": 0, "properly paired_passed": 42295408, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 42295408, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 42295408 }, "G176_M5_statistics_for_primary_reads": { "total_passed": 44603684, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 44603684, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44603684, "paired in sequencing_failed": 0, "read1_passed": 22301842, "read1_failed": 0, "read2_passed": 22301842, "read2_failed": 0, "properly paired_passed": 44603684, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44603684, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 44603684 }, "G176_M1_statistics_for_primary_reads": { "total_passed": 29796228, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29796228, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29796228, "paired in sequencing_failed": 0, "read1_passed": 14898114, "read1_failed": 0, "read2_passed": 14898114, "read2_failed": 0, "properly paired_passed": 29796228, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29796228, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29796228 }, "G176_M1_statistics_for_primary_unique_reads": { "total_passed": 28230700, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 28230700, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 28230700, "paired in sequencing_failed": 0, "read1_passed": 14115350, "read1_failed": 0, "read2_passed": 14115350, "read2_failed": 0, "properly paired_passed": 28230700, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 28230700, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 28230700 }, "G176_M1_statistics_for_all_accepted_reads": { "total_passed": 33223248, "total_failed": 0, "secondary_passed": 3427020, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33223248, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29796228, "paired in sequencing_failed": 0, "read1_passed": 14898114, "read1_failed": 0, "read2_passed": 14898114, "read2_failed": 0, "properly paired_passed": 29796228, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29796228, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33223248 }, "G176_M10_statistics_for_primary_unique_reads": { "total_passed": 25497262, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 25497262, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 25497262, "paired in sequencing_failed": 0, "read1_passed": 12748631, "read1_failed": 0, "read2_passed": 12748631, "read2_failed": 0, "properly paired_passed": 25497262, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 25497262, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 25497262 }, "G176_M10_statistics_for_all_accepted_reads": { "total_passed": 29087694, "total_failed": 0, "secondary_passed": 2242278, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29087694, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 26845416, "paired in sequencing_failed": 0, "read1_passed": 13422708, "read1_failed": 0, "read2_passed": 13422708, "read2_failed": 0, "properly paired_passed": 26845416, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 26845416, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29087694 }, "G176_M10_statistics_for_primary_reads": { "total_passed": 26845416, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 26845416, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 26845416, "paired in sequencing_failed": 0, "read1_passed": 13422708, "read1_failed": 0, "read2_passed": 13422708, "read2_failed": 0, "properly paired_passed": 26845416, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 26845416, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 26845416 }, "G176_M7_statistics_for_primary_reads": { "total_passed": 44990332, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 44990332, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44990332, "paired in sequencing_failed": 0, "read1_passed": 22495166, "read1_failed": 0, "read2_passed": 22495166, "read2_failed": 0, "properly paired_passed": 44990332, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44990332, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 44990332 }, "G176_M7_statistics_for_primary_unique_reads": { "total_passed": 43503792, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 43503792, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 43503792, "paired in sequencing_failed": 0, "read1_passed": 21751896, "read1_failed": 0, "read2_passed": 21751896, "read2_failed": 0, "properly paired_passed": 43503792, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 43503792, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 43503792 }, "G176_M7_statistics_for_all_accepted_reads": { "total_passed": 47588730, "total_failed": 0, "secondary_passed": 2598398, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 47588730, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 44990332, "paired in sequencing_failed": 0, "read1_passed": 22495166, "read1_failed": 0, "read2_passed": 22495166, "read2_failed": 0, "properly paired_passed": 44990332, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 44990332, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 47588730 }, "G176_M9_statistics_for_all_accepted_reads": { "total_passed": 21594844, "total_failed": 0, "secondary_passed": 1762472, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 21594844, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 19832372, "paired in sequencing_failed": 0, "read1_passed": 9916186, "read1_failed": 0, "read2_passed": 9916186, "read2_failed": 0, "properly paired_passed": 19832372, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 19832372, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 21594844 }, "G176_M9_statistics_for_primary_reads": { "total_passed": 19832372, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 19832372, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 19832372, "paired in sequencing_failed": 0, "read1_passed": 9916186, "read1_failed": 0, "read2_passed": 9916186, "read2_failed": 0, "properly paired_passed": 19832372, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 19832372, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 19832372 }, "G176_M9_statistics_for_primary_unique_reads": { "total_passed": 18937158, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 18937158, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 18937158, "paired in sequencing_failed": 0, "read1_passed": 9468579, "read1_failed": 0, "read2_passed": 9468579, "read2_failed": 0, "properly paired_passed": 18937158, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 18937158, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 18937158 }, "G176_M11_statistics_for_all_accepted_reads": { "total_passed": 34735060, "total_failed": 0, "secondary_passed": 2661790, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 34735060, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32073270, "paired in sequencing_failed": 0, "read1_passed": 16036635, "read1_failed": 0, "read2_passed": 16036635, "read2_failed": 0, "properly paired_passed": 32073270, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32073270, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 34735060 }, "G176_M11_statistics_for_primary_unique_reads": { "total_passed": 30410010, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30410010, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30410010, "paired in sequencing_failed": 0, "read1_passed": 15205005, "read1_failed": 0, "read2_passed": 15205005, "read2_failed": 0, "properly paired_passed": 30410010, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30410010, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30410010 }, "G176_M11_statistics_for_primary_reads": { "total_passed": 32073270, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 32073270, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32073270, "paired in sequencing_failed": 0, "read1_passed": 16036635, "read1_failed": 0, "read2_passed": 16036635, "read2_failed": 0, "properly paired_passed": 32073270, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32073270, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 32073270 }, "G176_M4_statistics_for_primary_unique_reads": { "total_passed": 30233622, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30233622, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30233622, "paired in sequencing_failed": 0, "read1_passed": 15116811, "read1_failed": 0, "read2_passed": 15116811, "read2_failed": 0, "properly paired_passed": 30233622, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30233622, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30233622 }, "G176_M4_statistics_for_all_accepted_reads": { "total_passed": 35553958, "total_failed": 0, "secondary_passed": 3648720, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35553958, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31905238, "paired in sequencing_failed": 0, "read1_passed": 15952619, "read1_failed": 0, "read2_passed": 15952619, "read2_failed": 0, "properly paired_passed": 31905238, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31905238, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35553958 }, "G176_M4_statistics_for_primary_reads": { "total_passed": 31905238, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 31905238, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31905238, "paired in sequencing_failed": 0, "read1_passed": 15952619, "read1_failed": 0, "read2_passed": 15952619, "read2_failed": 0, "properly paired_passed": 31905238, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31905238, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 31905238 }, "G176_M6_statistics_for_all_accepted_reads": { "total_passed": 27101554, "total_failed": 0, "secondary_passed": 2409650, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 27101554, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24691904, "paired in sequencing_failed": 0, "read1_passed": 12345952, "read1_failed": 0, "read2_passed": 12345952, "read2_failed": 0, "properly paired_passed": 24691904, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24691904, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 27101554 }, "G176_M6_statistics_for_primary_reads": { "total_passed": 24691904, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 24691904, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 24691904, "paired in sequencing_failed": 0, "read1_passed": 12345952, "read1_failed": 0, "read2_passed": 12345952, "read2_failed": 0, "properly paired_passed": 24691904, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 24691904, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 24691904 }, "G176_M6_statistics_for_primary_unique_reads": { "total_passed": 23473748, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 23473748, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 23473748, "paired in sequencing_failed": 0, "read1_passed": 11736874, "read1_failed": 0, "read2_passed": 11736874, "read2_failed": 0, "properly paired_passed": 23473748, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 23473748, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 23473748 }, "G176_M12_statistics_for_primary_unique_reads": { "total_passed": 29821284, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 29821284, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 29821284, "paired in sequencing_failed": 0, "read1_passed": 14910642, "read1_failed": 0, "read2_passed": 14910642, "read2_failed": 0, "properly paired_passed": 29821284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 29821284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 29821284 }, "G176_M12_statistics_for_all_accepted_reads": { "total_passed": 33615768, "total_failed": 0, "secondary_passed": 2441484, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33615768, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31174284, "paired in sequencing_failed": 0, "read1_passed": 15587142, "read1_failed": 0, "read2_passed": 15587142, "read2_failed": 0, "properly paired_passed": 31174284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31174284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33615768 }, "G176_M12_statistics_for_primary_reads": { "total_passed": 31174284, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 31174284, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 31174284, "paired in sequencing_failed": 0, "read1_passed": 15587142, "read1_failed": 0, "read2_passed": 15587142, "read2_failed": 0, "properly paired_passed": 31174284, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 31174284, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 31174284 }, "G176_M2_statistics_for_primary_reads": { "total_passed": 32276450, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 32276450, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32276450, "paired in sequencing_failed": 0, "read1_passed": 16138225, "read1_failed": 0, "read2_passed": 16138225, "read2_failed": 0, "properly paired_passed": 32276450, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32276450, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 32276450 }, "G176_M2_statistics_for_primary_unique_reads": { "total_passed": 30603658, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 30603658, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 30603658, "paired in sequencing_failed": 0, "read1_passed": 15301829, "read1_failed": 0, "read2_passed": 15301829, "read2_failed": 0, "properly paired_passed": 30603658, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 30603658, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 30603658 }, "G176_M2_statistics_for_all_accepted_reads": { "total_passed": 35834388, "total_failed": 0, "secondary_passed": 3557938, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35834388, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 32276450, "paired in sequencing_failed": 0, "read1_passed": 16138225, "read1_failed": 0, "read2_passed": 16138225, "read2_failed": 0, "properly paired_passed": 32276450, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 32276450, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35834388 }, "G176_M8_statistics_for_primary_reads": { "total_passed": 35283240, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 35283240, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 35283240, "paired in sequencing_failed": 0, "read1_passed": 17641620, "read1_failed": 0, "read2_passed": 17641620, "read2_failed": 0, "properly paired_passed": 35283240, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 35283240, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 35283240 }, "G176_M8_statistics_for_all_accepted_reads": { "total_passed": 37630380, "total_failed": 0, "secondary_passed": 2347140, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 37630380, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 35283240, "paired in sequencing_failed": 0, "read1_passed": 17641620, "read1_failed": 0, "read2_passed": 17641620, "read2_failed": 0, "properly paired_passed": 35283240, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 35283240, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 37630380 }, "G176_M8_statistics_for_primary_unique_reads": { "total_passed": 33882606, "total_failed": 0, "secondary_passed": 0, "secondary_failed": 0, "supplementary_passed": 0, "supplementary_failed": 0, "duplicates_passed": 0, "duplicates_failed": 0, "mapped_passed": 33882606, "mapped_failed": 0, "mapped_passed_pct": 100.0, "mapped_failed_pct": NaN, "paired in sequencing_passed": 33882606, "paired in sequencing_failed": 0, "read1_passed": 16941303, "read1_failed": 0, "read2_passed": 16941303, "read2_failed": 0, "properly paired_passed": 33882606, "properly paired_failed": 0, "properly paired_passed_pct": 100.0, "properly paired_failed_pct": NaN, "with itself and mate mapped_passed": 33882606, "with itself and mate mapped_failed": 0, "singletons_passed": 0, "singletons_failed": 0, "singletons_passed_pct": 0.0, "singletons_failed_pct": NaN, "with mate mapped to a different chr_passed": 0, "with mate mapped to a different chr_failed": 0, "with mate mapped to a different chr (mapQ >= 5)_passed": 0, "with mate mapped to a different chr (mapQ >= 5)_failed": 0, "flagstat_total": 33882606 } }, "multiqc_star": { "G176_M3_G176_M3": { "total_reads": 15369699.0, "avg_input_read_length": 300.0, "uniquely_mapped": 11716153.0, "uniquely_mapped_percent": 76.23, "avg_mapped_read_length": 286.74, "num_splices": 12660512.0, "num_annotated_splices": 12277600.0, "num_GTAG_splices": 12587323.0, "num_GCAG_splices": 61742.0, "num_ATAC_splices": 3892.0, "num_noncanonical_splices": 7555.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.28, "insertion_rate": 0.01, "insertion_length": 1.97, "multimapped": 560051.0, "multimapped_percent": 3.64, "multimapped_toomany": 34615.0, "multimapped_toomany_percent": 0.23, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 17.38, "unmapped_other_percent": 2.52, "unmapped_mismatches": 0, "unmapped_tooshort": 2671524, "unmapped_other": 387356 }, "G176_M13_G176_M13": { "total_reads": 16992425.0, "avg_input_read_length": 300.0, "uniquely_mapped": 13652168.0, "uniquely_mapped_percent": 80.34, "avg_mapped_read_length": 290.03, "num_splices": 13204101.0, "num_annotated_splices": 12743935.0, "num_GTAG_splices": 13115677.0, "num_GCAG_splices": 74092.0, "num_ATAC_splices": 4985.0, "num_noncanonical_splices": 9347.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.37, "insertion_rate": 0.02, "insertion_length": 2.06, "multimapped": 606669.0, "multimapped_percent": 3.57, "multimapped_toomany": 33906.0, "multimapped_toomany_percent": 0.2, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.8, "unmapped_other_percent": 2.09, "unmapped_mismatches": 0, "unmapped_tooshort": 2344595, "unmapped_other": 355087 }, "G176_M5_G176_M5": { "total_reads": 27035045.0, "avg_input_read_length": 300.0, "uniquely_mapped": 21147704.0, "uniquely_mapped_percent": 78.22, "avg_mapped_read_length": 289.67, "num_splices": 24164544.0, "num_annotated_splices": 23414703.0, "num_GTAG_splices": 24010075.0, "num_GCAG_splices": 131284.0, "num_ATAC_splices": 8267.0, "num_noncanonical_splices": 14918.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.25, "insertion_rate": 0.01, "insertion_length": 1.96, "multimapped": 1154138.0, "multimapped_percent": 4.27, "multimapped_toomany": 71979.0, "multimapped_toomany_percent": 0.27, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.19, "unmapped_other_percent": 4.05, "unmapped_mismatches": 0, "unmapped_tooshort": 3566215, "unmapped_other": 1095009 }, "G176_M1_G176_M1": { "total_reads": 19736008.0, "avg_input_read_length": 300.0, "uniquely_mapped": 14115350.0, "uniquely_mapped_percent": 71.52, "avg_mapped_read_length": 288.01, "num_splices": 14736469.0, "num_annotated_splices": 14278719.0, "num_GTAG_splices": 14647634.0, "num_GCAG_splices": 75668.0, "num_ATAC_splices": 4850.0, "num_noncanonical_splices": 8317.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.3, "insertion_rate": 0.01, "insertion_length": 1.96, "multimapped": 782764.0, "multimapped_percent": 3.97, "multimapped_toomany": 59441.0, "multimapped_toomany_percent": 0.3, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 16.77, "unmapped_other_percent": 7.44, "unmapped_mismatches": 0, "unmapped_tooshort": 3309982, "unmapped_other": 1468471 }, "G176_M10_G176_M10": { "total_reads": 16436531.0, "avg_input_read_length": 300.0, "uniquely_mapped": 12748631.0, "uniquely_mapped_percent": 77.56, "avg_mapped_read_length": 288.23, "num_splices": 13323078.0, "num_annotated_splices": 12906333.0, "num_GTAG_splices": 13240762.0, "num_GCAG_splices": 70318.0, "num_ATAC_splices": 4171.0, "num_noncanonical_splices": 7827.0, "mismatch_rate": 0.27, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 1.92, "multimapped": 674077.0, "multimapped_percent": 4.1, "multimapped_toomany": 26900.0, "multimapped_toomany_percent": 0.16, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 15.92, "unmapped_other_percent": 2.26, "unmapped_mismatches": 0, "unmapped_tooshort": 2615611, "unmapped_other": 371312 }, "G176_M7_G176_M7": { "total_reads": 27617494.0, "avg_input_read_length": 300.0, "uniquely_mapped": 21751896.0, "uniquely_mapped_percent": 78.76, "avg_mapped_read_length": 288.52, "num_splices": 19155883.0, "num_annotated_splices": 18567393.0, "num_GTAG_splices": 19065610.0, "num_GCAG_splices": 74230.0, "num_ATAC_splices": 4475.0, "num_noncanonical_splices": 11568.0, "mismatch_rate": 0.32, "deletion_rate": 0.02, "deletion_length": 2.45, "insertion_rate": 0.02, "insertion_length": 2.04, "multimapped": 743270.0, "multimapped_percent": 2.69, "multimapped_toomany": 39409.0, "multimapped_toomany_percent": 0.14, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 17.6, "unmapped_other_percent": 0.81, "unmapped_mismatches": 0, "unmapped_tooshort": 4859282, "unmapped_other": 223637 }, "G176_M9_G176_M9": { "total_reads": 12394901.0, "avg_input_read_length": 300.0, "uniquely_mapped": 9468579.0, "uniquely_mapped_percent": 76.39, "avg_mapped_read_length": 288.06, "num_splices": 10068199.0, "num_annotated_splices": 9773809.0, "num_GTAG_splices": 10007181.0, "num_GCAG_splices": 52449.0, "num_ATAC_splices": 3063.0, "num_noncanonical_splices": 5506.0, "mismatch_rate": 0.3, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 2.03, "multimapped": 447607.0, "multimapped_percent": 3.61, "multimapped_toomany": 26753.0, "multimapped_toomany_percent": 0.22, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 16.06, "unmapped_other_percent": 3.72, "unmapped_mismatches": 0, "unmapped_tooshort": 1990825, "unmapped_other": 461137 }, "G176_M11_G176_M11": { "total_reads": 19227077.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15205005.0, "uniquely_mapped_percent": 79.08, "avg_mapped_read_length": 288.63, "num_splices": 16290713.0, "num_annotated_splices": 15817966.0, "num_GTAG_splices": 16195720.0, "num_GCAG_splices": 79803.0, "num_ATAC_splices": 5078.0, "num_noncanonical_splices": 10112.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.55, "insertion_rate": 0.01, "insertion_length": 2.07, "multimapped": 831630.0, "multimapped_percent": 4.33, "multimapped_toomany": 24481.0, "multimapped_toomany_percent": 0.13, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 15.31, "unmapped_other_percent": 1.16, "unmapped_mismatches": 0, "unmapped_tooshort": 2942979, "unmapped_other": 222982 }, "G176_M4_G176_M4": { "total_reads": 20125707.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15116811.0, "uniquely_mapped_percent": 75.11, "avg_mapped_read_length": 288.98, "num_splices": 17152590.0, "num_annotated_splices": 16574210.0, "num_GTAG_splices": 17031562.0, "num_GCAG_splices": 103750.0, "num_ATAC_splices": 6831.0, "num_noncanonical_splices": 10447.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.25, "insertion_rate": 0.01, "insertion_length": 2.06, "multimapped": 835808.0, "multimapped_percent": 4.15, "multimapped_toomany": 66158.0, "multimapped_toomany_percent": 0.33, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.61, "unmapped_other_percent": 6.8, "unmapped_mismatches": 0, "unmapped_tooshort": 2738624, "unmapped_other": 1368306 }, "G176_M6_G176_M6": { "total_reads": 15118820.0, "avg_input_read_length": 300.0, "uniquely_mapped": 11736874.0, "uniquely_mapped_percent": 77.63, "avg_mapped_read_length": 290.16, "num_splices": 12754848.0, "num_annotated_splices": 12344596.0, "num_GTAG_splices": 12671392.0, "num_GCAG_splices": 70725.0, "num_ATAC_splices": 4739.0, "num_noncanonical_splices": 7992.0, "mismatch_rate": 0.29, "deletion_rate": 0.02, "deletion_length": 2.31, "insertion_rate": 0.01, "insertion_length": 2.04, "multimapped": 609078.0, "multimapped_percent": 4.03, "multimapped_toomany": 35430.0, "multimapped_toomany_percent": 0.23, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 12.71, "unmapped_other_percent": 5.39, "unmapped_mismatches": 0, "unmapped_tooshort": 1922256, "unmapped_other": 815182 }, "G176_M12_G176_M12": { "total_reads": 18558269.0, "avg_input_read_length": 300.0, "uniquely_mapped": 14910642.0, "uniquely_mapped_percent": 80.35, "avg_mapped_read_length": 289.07, "num_splices": 15462944.0, "num_annotated_splices": 14937250.0, "num_GTAG_splices": 15356604.0, "num_GCAG_splices": 90730.0, "num_ATAC_splices": 5476.0, "num_noncanonical_splices": 10134.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.28, "insertion_rate": 0.01, "insertion_length": 1.99, "multimapped": 676500.0, "multimapped_percent": 3.65, "multimapped_toomany": 31310.0, "multimapped_toomany_percent": 0.17, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 14.79, "unmapped_other_percent": 1.05, "unmapped_mismatches": 0, "unmapped_tooshort": 2744943, "unmapped_other": 194874 }, "G176_M2_G176_M2": { "total_reads": 20619409.0, "avg_input_read_length": 300.0, "uniquely_mapped": 15301829.0, "uniquely_mapped_percent": 74.21, "avg_mapped_read_length": 288.43, "num_splices": 16105855.0, "num_annotated_splices": 15585021.0, "num_GTAG_splices": 16005484.0, "num_GCAG_splices": 86265.0, "num_ATAC_splices": 5334.0, "num_noncanonical_splices": 8772.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.39, "insertion_rate": 0.01, "insertion_length": 1.97, "multimapped": 836396.0, "multimapped_percent": 4.06, "multimapped_toomany": 62711.0, "multimapped_toomany_percent": 0.3, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 14.72, "unmapped_other_percent": 6.7, "unmapped_mismatches": 0, "unmapped_tooshort": 3036411, "unmapped_other": 1382062 }, "G176_M8_G176_M8": { "total_reads": 20671637.0, "avg_input_read_length": 300.0, "uniquely_mapped": 16941303.0, "uniquely_mapped_percent": 81.95, "avg_mapped_read_length": 289.87, "num_splices": 18467987.0, "num_annotated_splices": 17945904.0, "num_GTAG_splices": 18365300.0, "num_GCAG_splices": 87327.0, "num_ATAC_splices": 5212.0, "num_noncanonical_splices": 10148.0, "mismatch_rate": 0.28, "deletion_rate": 0.02, "deletion_length": 2.36, "insertion_rate": 0.01, "insertion_length": 1.98, "multimapped": 700317.0, "multimapped_percent": 3.39, "multimapped_toomany": 28763.0, "multimapped_toomany_percent": 0.14, "unmapped_mismatches_percent": 0.0, "unmapped_tooshort_percent": 13.91, "unmapped_other_percent": 0.61, "unmapped_mismatches": 0, "unmapped_tooshort": 2875168, "unmapped_other": 126086 } }, "multiqc_general_stats": { "G176_M3_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 26745316, "Samtools_mqc-generalstats-samtools-mapped_passed": 26745316 }, "G176_M3_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 24552408, "Samtools_mqc-generalstats-samtools-mapped_passed": 24552408 }, "G176_M3_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 23432306, "Samtools_mqc-generalstats-samtools-mapped_passed": 23432306 }, "G176_M13_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 27304336, "Samtools_mqc-generalstats-samtools-mapped_passed": 27304336 }, "G176_M13_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 30735024, "Samtools_mqc-generalstats-samtools-mapped_passed": 30735024 }, "G176_M13_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 28517674, "Samtools_mqc-generalstats-samtools-mapped_passed": 28517674 }, "G176_M5_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 49228966, "Samtools_mqc-generalstats-samtools-mapped_passed": 49228966 }, "G176_M5_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 42295408, "Samtools_mqc-generalstats-samtools-mapped_passed": 42295408 }, "G176_M5_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 44603684, "Samtools_mqc-generalstats-samtools-mapped_passed": 44603684 }, "G176_M1_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 29796228, "Samtools_mqc-generalstats-samtools-mapped_passed": 29796228 }, "G176_M1_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 28230700, "Samtools_mqc-generalstats-samtools-mapped_passed": 28230700 }, "G176_M1_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 33223248, "Samtools_mqc-generalstats-samtools-mapped_passed": 33223248 }, "G176_M10_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 25497262, "Samtools_mqc-generalstats-samtools-mapped_passed": 25497262 }, "G176_M10_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 29087694, "Samtools_mqc-generalstats-samtools-mapped_passed": 29087694 }, "G176_M10_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 26845416, "Samtools_mqc-generalstats-samtools-mapped_passed": 26845416 }, "G176_M7_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 44990332, "Samtools_mqc-generalstats-samtools-mapped_passed": 44990332 }, "G176_M7_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 43503792, "Samtools_mqc-generalstats-samtools-mapped_passed": 43503792 }, "G176_M7_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 47588730, "Samtools_mqc-generalstats-samtools-mapped_passed": 47588730 }, "G176_M9_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 21594844, "Samtools_mqc-generalstats-samtools-mapped_passed": 21594844 }, "G176_M9_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 19832372, "Samtools_mqc-generalstats-samtools-mapped_passed": 19832372 }, "G176_M9_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 18937158, "Samtools_mqc-generalstats-samtools-mapped_passed": 18937158 }, "G176_M11_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 34735060, "Samtools_mqc-generalstats-samtools-mapped_passed": 34735060 }, "G176_M11_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 30410010, "Samtools_mqc-generalstats-samtools-mapped_passed": 30410010 }, "G176_M11_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 32073270, "Samtools_mqc-generalstats-samtools-mapped_passed": 32073270 }, "G176_M4_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 30233622, "Samtools_mqc-generalstats-samtools-mapped_passed": 30233622 }, "G176_M4_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 35553958, "Samtools_mqc-generalstats-samtools-mapped_passed": 35553958 }, "G176_M4_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 31905238, "Samtools_mqc-generalstats-samtools-mapped_passed": 31905238 }, "G176_M6_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 27101554, "Samtools_mqc-generalstats-samtools-mapped_passed": 27101554 }, "G176_M6_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 24691904, "Samtools_mqc-generalstats-samtools-mapped_passed": 24691904 }, "G176_M6_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 23473748, "Samtools_mqc-generalstats-samtools-mapped_passed": 23473748 }, "G176_M12_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 29821284, "Samtools_mqc-generalstats-samtools-mapped_passed": 29821284 }, "G176_M12_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 33615768, "Samtools_mqc-generalstats-samtools-mapped_passed": 33615768 }, "G176_M12_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 31174284, "Samtools_mqc-generalstats-samtools-mapped_passed": 31174284 }, "G176_M2_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 32276450, "Samtools_mqc-generalstats-samtools-mapped_passed": 32276450 }, "G176_M2_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 30603658, "Samtools_mqc-generalstats-samtools-mapped_passed": 30603658 }, "G176_M2_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 35834388, "Samtools_mqc-generalstats-samtools-mapped_passed": 35834388 }, "G176_M8_statistics_for_primary_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 35283240, "Samtools_mqc-generalstats-samtools-mapped_passed": 35283240 }, "G176_M8_statistics_for_all_accepted_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 37630380, "Samtools_mqc-generalstats-samtools-mapped_passed": 37630380 }, "G176_M8_statistics_for_primary_unique_reads": { "Samtools_mqc-generalstats-samtools-flagstat_total": 33882606, "Samtools_mqc-generalstats-samtools-mapped_passed": 33882606 }, "G176_M3_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.64378341593867, "featureCounts_mqc-generalstats-featurecounts-Assigned": 11205772 }, "G176_M13_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.21936735615911, "featureCounts_mqc-generalstats-featurecounts-Assigned": 12999508 }, "G176_M5_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 96.08836023050067, "featureCounts_mqc-generalstats-featurecounts-Assigned": 20320482 }, "G176_M1_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.3305798297598, "featureCounts_mqc-generalstats-featurecounts-Assigned": 13456245 }, "G176_M10_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 94.60687190648157, "featureCounts_mqc-generalstats-featurecounts-Assigned": 12061081 }, "G176_M7_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.60886554441048, "featureCounts_mqc-generalstats-featurecounts-Assigned": 20796741 }, "G176_M9_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.76708395209039, "featureCounts_mqc-generalstats-featurecounts-Assigned": 9067782 }, "G176_M11_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 94.06748633098114, "featureCounts_mqc-generalstats-featurecounts-Assigned": 14302966 }, "G176_M4_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 96.1957717140209, "featureCounts_mqc-generalstats-featurecounts-Assigned": 14541733 }, "G176_M6_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.79332622979508, "featureCounts_mqc-generalstats-featurecounts-Assigned": 11243142 }, "G176_M12_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.65018058913896, "featureCounts_mqc-generalstats-featurecounts-Assigned": 14262056 }, "G176_M2_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.57340498315594, "featureCounts_mqc-generalstats-featurecounts-Assigned": 14624479 }, "G176_M8_sorted": { "featureCounts_mqc-generalstats-featurecounts-percent_assigned": 95.70025989146171, "featureCounts_mqc-generalstats-featurecounts-Assigned": 16212871 }, "G176_M3_G176_M3": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 76.23, "STAR_mqc-generalstats-star-uniquely_mapped": 11716153.0 }, "G176_M13_G176_M13": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 80.34, "STAR_mqc-generalstats-star-uniquely_mapped": 13652168.0 }, "G176_M5_G176_M5": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 78.22, "STAR_mqc-generalstats-star-uniquely_mapped": 21147704.0 }, "G176_M1_G176_M1": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 71.52, "STAR_mqc-generalstats-star-uniquely_mapped": 14115350.0 }, "G176_M10_G176_M10": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 77.56, "STAR_mqc-generalstats-star-uniquely_mapped": 12748631.0 }, "G176_M7_G176_M7": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 78.76, "STAR_mqc-generalstats-star-uniquely_mapped": 21751896.0 }, "G176_M9_G176_M9": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 76.39, "STAR_mqc-generalstats-star-uniquely_mapped": 9468579.0 }, "G176_M11_G176_M11": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 79.08, "STAR_mqc-generalstats-star-uniquely_mapped": 15205005.0 }, "G176_M4_G176_M4": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 75.11, "STAR_mqc-generalstats-star-uniquely_mapped": 15116811.0 }, "G176_M6_G176_M6": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 77.63, "STAR_mqc-generalstats-star-uniquely_mapped": 11736874.0 }, "G176_M12_G176_M12": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 80.35, "STAR_mqc-generalstats-star-uniquely_mapped": 14910642.0 }, "G176_M2_G176_M2": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 74.21, "STAR_mqc-generalstats-star-uniquely_mapped": 15301829.0 }, "G176_M8_G176_M8": { "STAR_mqc-generalstats-star-uniquely_mapped_percent": 81.95, "STAR_mqc-generalstats-star-uniquely_mapped": 16941303.0 } } }, "config_analysis_dir_abs": [ "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES", "/projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/03_FASTQC", "/projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/06_CollectMetrics" ], "config_analysis_dir": [ "/projectnb/wax-dk/max/G174_G178_2024/G176/SAMPLES", "/projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/03_FASTQC/", "/projectnb/wax-dk/max/G174_G178_2024/G176/Scripts/06_CollectMetrics/" ], "config_creation_date": "2024-07-23, 12:55", "config_git_hash": null, "config_intro_text": null, "config_report_comment": null, "config_report_header_info": null, "config_script_path": "/projectnb/wax-es/routines/condaenv/multiqc/lib/python3.9/site-packages/multiqc/utils", "config_short_version": "1.11", "config_subtitle": null, "config_title": null, "config_version": "1.11" }