Sample Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent-2 Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent-1 phantompeakqualtools_mqc-generalstats-phantompeakqualtools-Estimated_Fragment_Length_bp Samtools Stats_mqc-generalstats-samtools_stats-error_rate-1 phantompeakqualtools_mqc-generalstats-phantompeakqualtools-NSC Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent-2 Picard (merged library; filtered)_mqc-generalstats-picard_merged_library_filtered-summed_median Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments-2 Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments-1 Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed-1 Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed-2 Samtools Stats_mqc-generalstats-samtools_stats-error_rate-2 Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent-1 Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent-2 Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped-1 Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped-2 Picard (merged library; filtered)_mqc-generalstats-picard_merged_library_filtered-PCT_PF_READS_ALIGNED Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent-1 Picard (merged library; filtered)_mqc-generalstats-picard_merged_library_filtered-summed_mean phantompeakqualtools_mqc-generalstats-phantompeakqualtools-RSC Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences-2 Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences-1 Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent Picard (merged library; filtered)_mqc-generalstats-picard_merged_library_filtered-PERCENT_DUPLICATION Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed Samtools Stats_mqc-generalstats-samtools_stats-error_rate Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent FastQC (library; trimmed)_mqc-generalstats-fastqc_library_trimmed-avg_sequence_length FastQC (library; trimmed)_mqc-generalstats-fastqc_library_trimmed-percent_duplicates FastQC (library; raw)_mqc-generalstats-fastqc_library_raw-percent_duplicates FastQC (library; trimmed)_mqc-generalstats-fastqc_library_trimmed-percent_gc FastQC (library; trimmed)_mqc-generalstats-fastqc_library_trimmed-percent_fails FastQC (library; raw)_mqc-generalstats-fastqc_library_raw-avg_sequence_length FastQC (library; trimmed)_mqc-generalstats-fastqc_library_trimmed-total_sequences cutadapt (library; trimmed)_mqc-generalstats-cutadapt_library_trimmed-percent_trimmed FastQC (library; raw)_mqc-generalstats-fastqc_library_raw-percent_fails FastQC (library; raw)_mqc-generalstats-fastqc_library_raw-percent_gc FastQC (library; raw)_mqc-generalstats-fastqc_library_raw-total_sequences featureCounts_mqc-generalstats-featurecounts-Assigned featureCounts_mqc-generalstats-featurecounts-percent_assigned SPT5_INPUT_R1 99.9168013119 94.2071639512 150 0.00059217 1.148937 100.0 155 0.0 0.0 187831 165868 0.000527531 10.9347690701 0.0 187831.0 165868.0 1.0 94.3362396287 158.011385 8.02834 165868.0 199108.0 SPT5_INPUT_R1_T1 187831.0 94.3362396287 0.000314 199108.0 187831 0.00059217 0.0 10.9347690701 94.2071639512 SPT5_INPUT_R1_T1_1 49.4508608393 2.54736123109 2.615 40.0 10.0 50.0 99554.0 1.1256 0.0 40.0 100000.0 SPT5_INPUT_R1_T1_2 49.3885127669 2.48809691223 2.538 40.0 10.0 50.0 99554.0 1.61022 0.0 40.0 100000.0 SPT5_INPUT_R2 99.8215285554 96.2758689974 155 0.000589508 1.137726 100.0 160 0.0 0.0 192118 171456 0.0005569978 10.3109302793 0.0 192118.0 171456.0 1.0 96.5029134016 163.122851 7.825372 171456.0 199080.0 SPT5_INPUT_R2_T1 192118.0 96.5029134016 0.00026 199080.0 192118 0.000589508 0.0 10.3109302793 96.2758689974 SPT5_INPUT_R2_T1_1 49.4474984931 1.6325095439 1.664 39.0 10.0 50.0 99540.0 1.1271 0.0 39.0 100000.0 SPT5_INPUT_R2_T1_2 49.3875627888 1.55013060076 1.568 39.0 10.0 50.0 99540.0 1.62362 0.0 39.0 100000.0 SPT5_T0_R1 99.827623357 94.9987970648 95 0.002564549 1.465785 100.0 118 0.0 0.0 190337 102102 0.001606342 42.8375235575 0.0 190337.0 102102.0 1.0 95.4012791211 165.024951 0.9126109 102102.0 199512.0 26454 51.8187694658 SPT5_T0_R1_T1 190337.0 95.4012791211 0.048036 199512.0 190337 0.002564549 0.0 42.8375235575 94.9987970648 SPT5_T0_R1_T1_1 67.7966438109 21.7039576567 29.602 43.0 9.09090909091 76.0 99756.0 10.3753157895 18.1818181818 43.0 100000.0 SPT5_T0_R1_T1_2 67.779461887 21.694935643 29.862 43.0 9.09090909091 76.0 99756.0 10.5560526316 18.1818181818 43.0 100000.0 SPT5_T0_R2 99.9318689064 92.578477585 95 0.002642268 1.555037 100.0 144 0.0 0.0 185423 85130 0.00178609 48.8983050847 0.0 185423.0 85130.0 1.0 92.9811453214 198.154229 0.9193525 85130.0 199420.0 22489 52.8344884295 SPT5_T0_R2_T1 185423.0 92.9811453214 0.057247 199420.0 185423 0.002642268 0.0 48.8983050847 92.578477585 SPT5_T0_R2_T1_1 68.7979340086 28.6932103099 37.139 43.0 9.09090909091 76.0 99710.0 9.08301315789 18.1818181818 43.0 100000.0 SPT5_T0_R2_T1_2 68.7311202487 28.5578176712 37.312 43.0 9.09090909091 76.0 99710.0 9.34567105263 18.1818181818 43.0 100000.0 SPT5_T15_R1 99.9452954048 94.2898094599 105 0.002263425 1.36137 100.0 164 0.0 0.0 188716 120648 0.001429953 32.6278703806 0.0 188716.0 120648.0 1.0 94.5764716495 192.658311 0.9332524 120648.0 199538.0 28536 47.3045554008 SPT5_T15_R1_T1 188716.0 94.5764716495 0.035551 199538.0 188716 0.002263425 0.0 32.6278703806 94.2898094599 SPT5_T15_R1_T1_1 71.5692249095 21.6520161573 26.581 43.0 9.09090909091 76.0 99769.0 5.45609210526 18.1818181818 43.0 100000.0 SPT5_T15_R1_T1_2 71.5532880955 21.6379837424 26.644 43.0 9.09090909091 76.0 99769.0 5.64297368421 18.1818181818 43.0 100000.0 SPT5_T15_R2 99.8469927566 94.0523577008 95 0.002551725 1.346095 100.0 124 0.0 0.0 188408 122870 0.001607864 31.1754915428 0.0 188408.0 122870.0 1.0 94.4524098379 174.667443 0.8935111 122870.0 199474.0 28721 46.7502238138 SPT5_T15_R2_T1 188408.0 94.4524098379 0.03209 199474.0 188408 0.002551725 0.0 31.1754915428 94.0523577008 SPT5_T15_R2_T1_1 68.9902042371 17.8088372419 23.455 42.0 9.09090909091 76.0 99737.0 8.80851315789 18.1818181818 42.0 100000.0 SPT5_T15_R2_T1_2 68.9680660136 17.761713306 23.511 42.0 9.09090909091 76.0 99737.0 9.03331578947 18.1818181818 42.0 100000.0