File Info

Filename
qc_metrics.csv
Full Path
s3://natera-rnd-pltf-dev-s3-gitlab-results/daq/build2793969/regression-run/63437016/reports/qc_metrics.csv
Size
16.4 KB
Workflow Run
gitlab-daq-build2793969-regression-run-63437016
Published
Jun 04, 2026 10:09 AM

Content

View in new tab
sample_id mosdepth_mean_coverage mosdepth_mean_coverage_target samtools_raw_total_sequences samtools_reads_mapped samtools_reads_unmapped samtools_reads_properly_paired samtools_reads_duplicated samtools_reads_mq0 samtools_bases_mapped_cigar samtools_mismatches samtools_error_rate samtools_average_length samtools_average_quality samtools_insert_size_average samtools_insert_size_std_dev samtools_properly_paired_percent samtools_duplication_rate samtools_mapping_rate sentieon_insert_size_median_insert_size sentieon_insert_size_mean_insert_size sentieon_hotspot_depth_mean_target_coverage sentieon_hotspot_depth_pct_selected_bases sentieon_hotspot_depth_zero_cvg_targets_pct sentieon_hotspot_depth_pct_target_bases_10x sentieon_hotspot_depth_pct_target_bases_20x sentieon_hotspot_depth_pct_target_bases_30x sentieon_hotspot_depth_at_dropout sentieon_hotspot_depth_gc_dropout sentieon_coding_depth_mean_target_coverage sentieon_coding_depth_pct_selected_bases sentieon_coding_depth_zero_cvg_targets_pct sentieon_coding_depth_pct_target_bases_10x sentieon_coding_depth_pct_target_bases_20x sentieon_coding_depth_pct_target_bases_30x sentieon_coding_depth_at_dropout sentieon_coding_depth_gc_dropout sentieon_noncoding_depth_mean_target_coverage sentieon_noncoding_depth_pct_selected_bases sentieon_noncoding_depth_zero_cvg_targets_pct sentieon_noncoding_depth_pct_target_bases_10x sentieon_noncoding_depth_pct_target_bases_20x sentieon_noncoding_depth_pct_target_bases_30x sentieon_noncoding_depth_at_dropout sentieon_noncoding_depth_gc_dropout sentieon_boosted_depth_mean_target_coverage sentieon_boosted_depth_pct_selected_bases sentieon_boosted_depth_zero_cvg_targets_pct sentieon_boosted_depth_pct_target_bases_10x sentieon_boosted_depth_pct_target_bases_20x sentieon_boosted_depth_pct_target_bases_30x sentieon_boosted_depth_at_dropout sentieon_boosted_depth_gc_dropout sentieon_non_boosted_depth_mean_target_coverage sentieon_non_boosted_depth_pct_selected_bases sentieon_non_boosted_depth_zero_cvg_targets_pct sentieon_non_boosted_depth_pct_target_bases_10x sentieon_non_boosted_depth_pct_target_bases_20x sentieon_non_boosted_depth_pct_target_bases_30x sentieon_non_boosted_depth_at_dropout sentieon_non_boosted_depth_gc_dropout sentieon_foresight_depth_mean_target_coverage sentieon_foresight_depth_pct_selected_bases sentieon_foresight_depth_zero_cvg_targets_pct sentieon_foresight_depth_pct_target_bases_10x sentieon_foresight_depth_pct_target_bases_20x sentieon_foresight_depth_pct_target_bases_30x sentieon_foresight_depth_at_dropout sentieon_foresight_depth_gc_dropout sentieon_all_targets_mean_target_coverage sentieon_all_targets_pct_selected_bases sentieon_all_targets_zero_cvg_targets_pct sentieon_all_targets_pct_target_bases_10x sentieon_all_targets_pct_target_bases_20x sentieon_all_targets_pct_target_bases_30x sentieon_all_targets_at_dropout sentieon_all_targets_gc_dropout sentieon_all_probes_mean_target_coverage sentieon_all_probes_pct_selected_bases sentieon_all_probes_zero_cvg_targets_pct sentieon_all_probes_pct_target_bases_10x sentieon_all_probes_pct_target_bases_20x sentieon_all_probes_pct_target_bases_30x sentieon_all_probes_at_dropout sentieon_all_probes_gc_dropout seqtool_hotspot_depth_frac_reads_on_target seqtool_hotspot_depth_frac_pairs_on_target seqtool_hotspot_depth_frag_size_median seqtool_hotspot_depth_frag_size_mean seqtool_hotspot_depth_frag_size_std seqtool_hotspot_depth_min_depth seqtool_hotspot_depth_mean_depth seqtool_hotspot_depth_cv_depth seqtool_hotspot_depth_max_depth seqtool_hotspot_depth_q5_depth seqtool_hotspot_depth_q50_depth seqtool_hotspot_depth_frac_bases_gt30x seqtool_hotspot_depth_frac_bases_gt100x seqtool_hotspot_depth_contam seqtool_hotspot_depth_saturation_at_1000000_reads seqtool_coding_depth_frac_reads_on_target seqtool_coding_depth_frac_pairs_on_target seqtool_coding_depth_frag_size_median seqtool_coding_depth_frag_size_mean seqtool_coding_depth_frag_size_std seqtool_coding_depth_min_depth seqtool_coding_depth_mean_depth seqtool_coding_depth_cv_depth seqtool_coding_depth_max_depth seqtool_coding_depth_q5_depth seqtool_coding_depth_q50_depth seqtool_coding_depth_frac_bases_gt30x seqtool_coding_depth_frac_bases_gt100x seqtool_coding_depth_contam seqtool_coding_depth_saturation_at_1000000_reads seqtool_coding_depth_gc_bias_mae seqtool_coding_depth_gc_bias_low seqtool_coding_depth_gc_bias_high seqtool_coding_depth_gc_bias_ratio seqtool_noncoding_depth_frac_reads_on_target seqtool_noncoding_depth_frac_pairs_on_target seqtool_noncoding_depth_frag_size_median seqtool_noncoding_depth_frag_size_mean seqtool_noncoding_depth_frag_size_std seqtool_noncoding_depth_min_depth seqtool_noncoding_depth_mean_depth seqtool_noncoding_depth_cv_depth seqtool_noncoding_depth_max_depth seqtool_noncoding_depth_q5_depth seqtool_noncoding_depth_q50_depth seqtool_noncoding_depth_frac_bases_gt30x seqtool_noncoding_depth_frac_bases_gt100x seqtool_noncoding_depth_contam seqtool_noncoding_depth_saturation_at_1000000_reads seqtool_noncoding_depth_gc_bias_mae seqtool_noncoding_depth_gc_bias_low seqtool_noncoding_depth_gc_bias_high seqtool_noncoding_depth_gc_bias_ratio seqtool_boosted_depth_frac_reads_on_target seqtool_boosted_depth_frac_pairs_on_target seqtool_boosted_depth_frag_size_median seqtool_boosted_depth_frag_size_mean seqtool_boosted_depth_frag_size_std seqtool_boosted_depth_min_depth seqtool_boosted_depth_mean_depth seqtool_boosted_depth_cv_depth seqtool_boosted_depth_max_depth seqtool_boosted_depth_q5_depth seqtool_boosted_depth_q50_depth seqtool_boosted_depth_frac_bases_gt30x seqtool_boosted_depth_frac_bases_gt100x seqtool_boosted_depth_contam seqtool_boosted_depth_saturation_at_1000000_reads seqtool_boosted_depth_gc_bias_mae seqtool_boosted_depth_gc_bias_low seqtool_boosted_depth_gc_bias_high seqtool_boosted_depth_gc_bias_ratio seqtool_non_boosted_depth_frac_reads_on_target seqtool_non_boosted_depth_frac_pairs_on_target seqtool_non_boosted_depth_frag_size_median seqtool_non_boosted_depth_frag_size_mean seqtool_non_boosted_depth_frag_size_std seqtool_non_boosted_depth_min_depth seqtool_non_boosted_depth_mean_depth seqtool_non_boosted_depth_cv_depth seqtool_non_boosted_depth_max_depth seqtool_non_boosted_depth_q5_depth seqtool_non_boosted_depth_q50_depth seqtool_non_boosted_depth_frac_bases_gt30x seqtool_non_boosted_depth_frac_bases_gt100x seqtool_non_boosted_depth_contam seqtool_non_boosted_depth_saturation_at_1000000_reads seqtool_non_boosted_depth_gc_bias_mae seqtool_non_boosted_depth_gc_bias_low seqtool_non_boosted_depth_gc_bias_high seqtool_non_boosted_depth_gc_bias_ratio seqtool_foresight_depth_frac_reads_on_target seqtool_foresight_depth_frac_pairs_on_target seqtool_foresight_depth_frag_size_median seqtool_foresight_depth_frag_size_mean seqtool_foresight_depth_frag_size_std seqtool_foresight_depth_min_depth seqtool_foresight_depth_mean_depth seqtool_foresight_depth_cv_depth seqtool_foresight_depth_max_depth seqtool_foresight_depth_q5_depth seqtool_foresight_depth_q50_depth seqtool_foresight_depth_frac_bases_gt30x seqtool_foresight_depth_frac_bases_gt100x seqtool_foresight_depth_contam seqtool_foresight_depth_saturation_at_1000000_reads seqtool_foresight_depth_gc_bias_mae seqtool_foresight_depth_gc_bias_low seqtool_foresight_depth_gc_bias_high seqtool_foresight_depth_gc_bias_ratio seqtool_all_targets_frac_reads_on_target seqtool_all_targets_frac_pairs_on_target seqtool_all_targets_frag_size_median seqtool_all_targets_frag_size_mean seqtool_all_targets_frag_size_std seqtool_all_targets_min_depth seqtool_all_targets_mean_depth seqtool_all_targets_cv_depth seqtool_all_targets_max_depth seqtool_all_targets_q5_depth seqtool_all_targets_q50_depth seqtool_all_targets_frac_bases_gt30x seqtool_all_targets_frac_bases_gt100x seqtool_all_targets_contam seqtool_all_targets_saturation_at_1000000_reads seqtool_all_targets_gc_bias_mae seqtool_all_targets_gc_bias_low seqtool_all_targets_gc_bias_high seqtool_all_targets_gc_bias_ratio seqtool_all_probes_frac_reads_on_target seqtool_all_probes_frac_pairs_on_target seqtool_all_probes_frag_size_median seqtool_all_probes_frag_size_mean seqtool_all_probes_frag_size_std seqtool_all_probes_min_depth seqtool_all_probes_mean_depth seqtool_all_probes_cv_depth seqtool_all_probes_max_depth seqtool_all_probes_q5_depth seqtool_all_probes_q50_depth seqtool_all_probes_frac_bases_gt30x seqtool_all_probes_frac_bases_gt100x seqtool_all_probes_contam seqtool_all_probes_saturation_at_1000000_reads seqtool_all_probes_gc_bias_mae seqtool_all_probes_gc_bias_low seqtool_all_probes_gc_bias_high seqtool_all_probes_gc_bias_ratio
HCC1395_BL 0.03 1.35 999992 999983 9 999292 146553 129468 144029228 614526 0.004266676 144.0 38.9 304.8 148.7 99.9 0.14655417243337945 0.9999909999279994 275 301.72527 0.0 0.777421 1.0 0.0 0.0 0.0 0.0 0.0 0.873883 0.777421 0.995655 0.00308548 0.00308548 0.00308548 37.322 22.308 6.18819 0.777421 0.993766 0.0127569 0.0127121 0.0126975 53.8859 14.9069 4.49156 0.777421 0.994302 0.00966925 0.00963876 0.0096288 46.5416 19.3933 0.83452 0.777421 0.990102 0.00976176 0.00971191 0.00958401 10.459 5.36945 0.611165 0.777421 0.988625 0.00696598 0.0068551 0.00664833 40.6509 28.8673 1.32444 0.777421 0.990202 0.00972054 0.00967173 0.00955708 16.4787 12.4848 1.17401 0.777421 0.990252 0.00980531 0.00969251 0.00934613 20.487 10.0409 0.0 0.0 275.0 301.595461 123.55658 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 31.0 0.030424 0.042904 275.0 301.595461 123.55658 0.0 0.879222 1.995704 582.0 0.0 0.0 0.003893 0.003373 0.0 31.0 1.1857425454545454 0.0704068 2.1941016666666666 0.002942331204755775 0.237115 0.248213 275.0 301.595461 123.55658 0.0 5.741505 1.963404 744.0 0.0 0.0 0.01444 0.013785 0.0 31.0 0.9694863636363635 0.4690562 1.102307 0.02062572049867201 0.252801 0.263975 275.0 301.595461 123.55658 0.0 4.188256 1.942377 744.0 0.0 0.0 0.011071 0.010459 0.0 31.0 0.8147175454545454 0.1027012 0.8331733333333333 0.006402561403243031 0.424765 0.519157 275.0 301.595461 123.55658 0.0 0.712114 1.717744 412.0 0.0 0.0 0.009799 0.001376 0.0 31.0 0.35874599999999995 0.5043894 1.3692595 0.7768160245659063 0.007957 0.009671 275.0 301.595461 123.55658 0.0 0.705061 1.987368 257.0 0.0 0.0 0.007269 0.002275 0.0 31.0 0.8502152727272727 0.189811 1.3193543333333333 0.743582268899425 0.672452 0.772698 275.0 301.595461 123.55658 0.0 1.179182 1.736714 744.0 0.0 0.0 0.009939 0.0026 0.0 31.0 0.35817618181818184 0.3204236 1.0567951666666666 0.4441745910026099 0.695524 0.775208 275.0 301.595461 123.55658 0.0 1.046143 1.678139 744.0 0.0 0.0 0.009497 0.00216 0.0 31.0 0.35609945454545455 0.42917000000000005 0.9477595 0.564517690362007
HCC1395_tumor 0.03 1.27 999980 999976 4 998864 169120 130024 143510476 699130 0.00487163 144.0 38.9 296.6 145.3 99.9 0.16912338246764935 0.9999959999199984 265 292.071073 0.0 0.773814 1.0 0.0 0.0 0.0 0.0 0.0 0.698404 0.773814 0.995231 0.00308548 0.00308548 0.00307018 36.5984 21.9637 5.45997 0.773814 0.993574 0.0127564 0.0127104 0.0126823 53.4103 14.9579 3.93981 0.773814 0.994077 0.00966886 0.00963759 0.00961355 46.0726 19.5883 0.843406 0.773814 0.990107 0.00975451 0.009658 0.00944918 10.8043 4.80992 0.522356 0.773814 0.988625 0.00698396 0.00660637 0.00622279 40.7917 29.5779 1.25712 0.773814 0.990192 0.00971458 0.00962097 0.00943303 15.7673 10.8893 1.12248 0.773814 0.990245 0.00978973 0.00960264 0.00919073 19.7867 8.30093 0.0 0.0 265.0 291.923995 119.878181 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 22.0 0.026551 0.03713 265.0 291.923995 119.878181 0.0 0.728002 2.005771 508.0 0.0 0.0 0.003892 0.002984 0.0 22.0 1.204762181818182 0.08127039999999999 2.2583365 0.005553820499665527 0.218128 0.227585 265.0 291.923995 119.878181 0.0 5.076311 1.946193 622.0 0.0 0.0 0.014491 0.013702 0.0 22.0 0.9678070909090909 0.43608159999999996 1.1109391666666666 0.019781256844446926 0.230929 0.240205 265.0 291.923995 119.878181 0.0 3.687251 2.011725 622.0 0.0 0.0 0.011105 0.010279 0.0 22.0 0.8075224545454546 0.1151022 0.8421403333333334 0.004588874144762227 0.445619 0.539071 265.0 291.923995 119.878181 0.0 0.718654 1.711118 376.0 0.0 0.0 0.009642 0.001608 0.0 22.0 0.4005874545454546 0.46470700000000004 1.4002976666666667 0.7345906772734074 0.007187 0.00871 265.0 291.923995 119.878181 0.0 0.615946 1.986219 241.0 0.0 0.0 0.006712 0.001489 0.0 22.0 0.8531469090909091 0.181196 1.3210856666666666 0.6627888087414251 0.67209 0.770536 265.0 291.923995 119.878181 0.0 1.116645 1.777627 622.0 0.0 0.0 0.009802 0.002771 0.0 22.0 0.34322345454545455 0.3195652 1.0908101666666667 0.435355516016543 0.695869 0.773538 265.0 291.923995 119.878181 0.0 0.997416 1.358546 622.0 0.0 0.0 0.009349 0.002338 0.0 22.0 0.33228463636363637 0.42950299999999997 0.9709880000000001 0.5542473939581553
Sig_18_Blood 0.03 1.45 999982 999975 7 999480 115575 123440 144627827 649292 0.004489399 145.0 38.9 312.7 151.8 99.9 0.11557708038744698 0.9999929998739977 280 307.472641 0.0 0.784477 1.0 0.0 0.0 0.0 0.0 0.0 0.915509 0.784477 0.995443 0.00321527 0.00313017 0.00311426 37.2112 21.5116 7.09592 0.784477 0.993383 0.0132399 0.0131342 0.0130552 53.976 14.9504 5.12278 0.784477 0.994077 0.0100394 0.00994034 0.00988151 46.7068 19.5302 0.846148 0.784477 0.989979 0.0097916 0.00972018 0.00961445 9.15578 5.78684 0.573986 0.784477 0.988625 0.00697947 0.00667979 0.00643406 40.4455 29.2768 1.41939 0.784477 0.990058 0.0097963 0.00971643 0.00961382 16.1767 14.118 1.25552 0.784477 0.99013 0.00988723 0.00976112 0.00945576 20.0992 12.029 0.0 0.0 280.0 307.417657 125.665527 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 27.0 0.030647 0.044265 280.0 307.417657 125.665527 0.0 0.902486 1.981796 586.0 0.0 0.0 0.003835 0.003405 0.0 27.0 1.1127487272727272 0.078514 2.083718333333333 0.012995241826873685 0.257706 0.269489 280.0 307.417657 125.665527 0.0 6.517132 1.99418 806.0 0.0 0.0 0.01456 0.014116 0.0 27.0 0.9520144545454545 0.48518019999999995 1.0816221666666666 0.021396313662784414 0.273051 0.284774 280.0 307.417657 125.665527 0.0 4.723542 1.942057 806.0 0.0 0.0 0.011134 0.010694 0.0 27.0 0.8184688181818182 0.1057968 0.8187665000000001 0.007868670402711258 0.413797 0.509401 280.0 307.417657 125.665527 0.0 0.723479 1.70641 422.0 0.0 0.0 0.009914 0.001434 0.0 27.0 0.30123545454545453 0.5475152 1.2997915 0.8896864478456759 0.007347 0.009057 280.0 307.417657 125.665527 0.0 0.666941 1.98342 266.0 0.0 0.0 0.007062 0.001774 0.0 27.0 0.8436132727272727 0.1837324 1.2919105 0.7921682306770069 0.681791 0.783822 280.0 307.417657 125.665527 0.0 1.261013 1.689229 806.0 0.0 0.0 0.010043 0.002682 0.0 27.0 0.35040327272727273 0.34580219999999995 1.0101778333333333 0.4833793927990435 0.704681 0.786191 280.0 307.417657 125.665527 0.0 1.116617 1.635608 806.0 0.0 0.0 0.009656 0.002236 0.0 27.0 0.3527551818181818 0.4740154 0.918126 0.6198030152776968
Sig_18_tissue 0.03 1.45 999980 999972 8 998956 84376 118922 141233489 719956 0.00509763 142.0 39.1 244.5 117.4 99.9 0.08437768755375108 0.9999919998399968 218 241.995101 0.0 0.810994 1.0 0.0 0.0 0.0 0.0 0.0 1.05221 0.810994 0.995231 0.00320241 0.00306773 0.003061 37.8895 21.4249 7.00156 0.810994 0.992999 0.0130432 0.012955 0.0128678 53.212 14.8298 5.10219 0.810994 0.993627 0.00990145 0.00979845 0.00973688 46.5452 19.083 0.966277 0.810994 0.989984 0.00974931 0.00969906 0.00954547 9.88838 5.62863 0.53582 0.810994 0.98912 0.00688507 0.00646403 0.00610142 41.4845 28.6591 1.5194 0.810994 0.990039 0.00973979 0.0096774 0.00953145 16.0088 12.9104 1.34833 0.810994 0.99013 0.00982312 0.00967753 0.0093349 20.1829 10.9407 0.0 0.0 218.0 241.867831 94.874466 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 36.0 0.034384 0.043198 218.0 241.867831 94.874466 0.0 1.03117 1.97026 693.0 0.0 0.0 0.003842 0.003574 0.0 36.0 1.0305081818181818 0.0718778 1.9561171666666668 0.013131859287723471 0.258294 0.266334 218.0 241.867831 94.874466 0.0 6.371626 1.957437 843.0 0.0 0.0 0.014554 0.014151 0.0 36.0 0.9499222727272727 0.4822058 1.0125951666666666 0.020609028741837624 0.276479 0.284204 218.0 241.867831 94.874466 0.0 4.665626 1.952069 843.0 0.0 0.0 0.011132 0.010772 0.0 36.0 0.8208596363636363 0.11167679999999999 0.7712463333333334 0.010112587837394103 0.467734 0.529275 218.0 241.867831 94.874466 0.0 0.805977 1.634082 357.0 0.0 0.0 0.009737 0.002489 0.0 36.0 0.2860910909090909 0.46839820000000004 1.2239436666666668 0.6969100292527867 0.007739 0.008725 218.0 241.867831 94.874466 0.0 0.68359 1.987347 343.0 0.0 0.0 0.006771 0.001753 0.0 36.0 0.8351928181818181 0.1678402 1.2622161666666667 0.6362426246423203 0.73813 0.803331 218.0 241.867831 94.874466 0.0 1.323868 1.656403 843.0 0.0 0.0 0.009886 0.003597 0.0 36.0 0.3827044545454546 0.3160078 0.9551683333333333 0.4107619911842601 0.757759 0.8063 218.0 241.867831 94.874466 0.0 1.174775 1.604051 843.0 0.0 0.0 0.009514 0.00299 0.0 36.0 0.4341488181818182 0.43715840000000006 0.8745094999999999 0.5928870163264042
5 rows