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qc_metrics.csv
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s3://natera-platform-sandbox/projects/lcvs/flowcells/20260529_LH00995_0049_B23YT2HLT4/reports/qc_metrics.csv
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7.7 KB
Workflow Run
pgrauman-main-nf-260606t153514
Published
Jun 06, 2026 2:58 PM

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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 sentieon_prenatal_exome_v1_targets_mean_target_coverage sentieon_prenatal_exome_v1_targets_pct_selected_bases sentieon_prenatal_exome_v1_targets_zero_cvg_targets_pct sentieon_prenatal_exome_v1_targets_pct_target_bases_10x sentieon_prenatal_exome_v1_targets_pct_target_bases_20x sentieon_prenatal_exome_v1_targets_pct_target_bases_30x sentieon_prenatal_exome_v1_targets_at_dropout sentieon_prenatal_exome_v1_targets_gc_dropout
10PercentHG514 0.56 20.67 45343264 45342206 1058 44463932 30176010 2095124 6312170877 18932839 0.002999418 139.0 39.4 320.7 161.6 98.1 0.6655014954371172 0.9999766668760326 21.4008 0.865476 0.00899447 0.873134 0.436841 0.150477 3.4006 0.403849
10PercentNA24385 44.26 1569.99 4701118100 4701007218 110882 4627432294 3437706590 212976722 644605662664 1800625518 0.002793375 137.0 39.5 266.2 134.2 98.4 0.7312529736276994 0.9999764136961375 1688.36 0.876494 0.00571528 0.990796 0.98976 0.989104 3.00048 0.240992
13432478-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
13511611-cfDNA 26.59 1039.62 2779412168 2779337889 74279 2732438882 1916703511 127489596 391181640793 1123527407 0.002872138 140.0 39.5 219.3 114.7 98.3 0.6896075123608655 0.999973275284301 1132.44 0.878188 0.00720235 0.988582 0.987458 0.986738 0.117061 1.6586
13739430-cfDNA 0.11 4.42 7645232 7645138 94 7500176 4116991 338449 1078620007 3216106 0.002981686 141.0 39.5 226.8 123.6 98.1 0.5385043907104454 0.9999877047550683 4.73787 0.877424 0.0348763 0.0811484 0.0105429 0.00408489 0.0841164 3.88757
13929215-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
14138939-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
14389853-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
14558439-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
14668865-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
14862332-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
15451964-cfDNA 22.98 916.63 2937398860 2937310815 88045 2569982228 2150310552 139409882 408989588072 1153044496 0.002819251 139.0 39.5 197.8 102.8 87.5 0.7320458182515942 0.9999700262020256 1028.4 0.883428 0.00863859 0.986306 0.985163 0.984484 0.0915372 1.16466
15921737-cfDNA 0.11 4.59 10637896 10637695 201 10457032 6994708 495042 1497143477 4571779 0.003053668 140.0 39.5 233.1 125.1 98.3 0.6575273907547131 0.9999811052862333 4.77615 0.875462 0.0360668 0.0820325 0.0110678 0.00450978 0.0827686 3.43982
16098090-cfDNA 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
1_25PercentHG514 41.44 1461.87 4786699986 4786541621 158365 4715730758 3607854727 216555050 658031806902 1887564323 0.0028685 137.0 39.5 269.4 133.9 98.5 0.7537248495941145 0.999966915620268 1569.32 0.877618 0.00674055 0.989651 0.9886 0.987954 3.56347 0.226716
1_25PercentNA24385 17.56 655.87 1644948546 1644916857 31689 1622076210 1137743993 73495053 225582495803 617202423 0.002736039 137.0 39.5 263.7 131.5 98.6 0.6916593201450814 0.9999807355676401 705.523 0.878307 0.00636349 0.988268 0.987051 0.986408 2.84225 0.293378
20PercentHG514 37.65 1333.77 3584950312 3584823013 127299 3531869482 2514340968 161848317 494611109091 1452968371 0.002937597 138.0 39.5 274.8 135.7 98.5 0.7013600605798299 0.9999644907212315 1433.26 0.876003 0.00672361 0.989751 0.988692 0.98803 3.64652 0.212078
20PercentNA24385 41.36 1485.09 4057683532 4057391515 292017 3995074088 2868372725 184574935 557391975413 1598848680 0.002868446 137.0 39.5 265.0 130.9 98.5 0.7068990724336262 0.9999280335694746 1603.19 0.876975 0.0057407 0.990672 0.989585 0.988921 3.50153 0.22767
2_5PercentHG514 41.67 1463.52 4777635264 4777509835 125429 4704613476 3595239533 216088560 656746673407 1870434570 0.002848031 137.0 39.5 272.2 136.5 98.5 0.7525144416298414 0.9999737466355071 1568.45 0.876785 0.00664311 0.989771 0.988679 0.988037 3.45874 0.22326
2_5PercentNA24385 38.7 1391.24 3476405506 3476306350 99156 3423188882 2368837975 157304984 478870051061 1360743402 0.002841571 137.0 39.5 271.7 134.2 98.5 0.6814043905153107 0.9999714774355786 1499.6 0.87607 0.00581272 0.990413 0.988962 0.987936 3.34579 0.193391
3140_NA24143 37.73 1344.59 3363182662 3363094030 88632 3309041536 2298093088 153009135 463754490776 1329172280 0.002866112 137.0 39.5 280.0 140.3 98.4 0.6833090316401018 0.9999736463912586 1438.6 0.873763 0.00681681 0.989506 0.988491 0.987816 3.46178 0.220059
3140_NA24385 48.38 1573.99 5352361062 5352220283 140779 5236956012 4089597847 255356823 748261026864 2251965300 0.003009598 139.0 39.4 340.1 170.7 97.8 0.7640736115571121 0.9999736977759218 1616.93 0.859972 0.00503317 0.991649 0.990712 0.990034 3.66311 0.354251
40PercentHG514 24.21 874.99 2434505476 2434448066 57410 2393885668 1744881342 111332090 334644132780 956588630 0.002858525 137.0 39.5 272.2 136.3 98.3 0.7167292738510973 0.9999764182087221 936.761 0.876409 0.00688036 0.989068 0.988001 0.987367 3.80016 0.268857
40PercentNA24385 10.07 385.6 810559176 810532199 26977 799600494 517291645 36357166 111381576066 310477018 0.002787508 137.0 39.5 263.1 128.9 98.6 0.6381910911832056 0.9999667180376229 416.32 0.878506 0.00652025 0.988454 0.987343 0.98649 2.9546 0.347378
5PercentHG514 19.01 700.83 1597446062 1597411196 34866 1574063560 1055172273 72008926 220182909473 638470747 0.002899729 137.0 39.5 276.1 137.1 98.5 0.6605370272589522 0.9999781739109511 751.52 0.875829 0.00702441 0.98862 0.987484 0.986845 3.48467 0.300566
5PercentNA24385 44.52 1557.08 4725085206 4724950420 134786 4646372032 3474484478 214488130 651023146963 1845677806 0.002835042 137.0 39.5 278.0 139.2 98.3 0.7353273700944135 0.9999714743768369 1660.99 0.873931 0.00562207 0.990888 0.989793 0.989059 3.29993 0.217488
D0000162_22q 0.0 0.0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
D0000476_22q 16.66 570.0 3217517070 3217392669 124401 2891403072 2675308535 162994061 450036254611 1348396701 0.002996196 140.0 39.5 202.8 104.8 89.9 0.8314823128506355 0.9999613363356609 619.71 0.875754 0.00748621 0.987467 0.986212 0.98525 0.0584103 3.85839
D0001109_22q 20.19 713.86 2910792518 2910697565 94953 2823108928 2265151375 139445230 409535043694 1249461958 0.003050928 140.0 39.5 216.8 113.3 97.0 0.7781905996365489 0.9999673789871958 770.704 0.876049 0.00628723 0.989168 0.98782 0.986965 0.0585233 2.89857
D0001483_22q 23.92 851.22 4092956436 4092824135 132301 3893807774 3323389965 197793630 573408582572 1671273595 0.002914629 140.0 39.5 210.6 111.2 95.1 0.8119778494998865 0.9999676759325273 932.742 0.878578 0.0065499 0.989022 0.987716 0.986762 1.02084 0.43738
SH032_HG513 11.7 436.55 803021270 803002871 18399 789881172 472039399 36499147 111118197690 334674303 0.003011877 138.0 39.5 287.6 143.6 98.4 0.5878292601141187 0.9999770877800036 466.442 0.871586 0.00733793 0.987906 0.986863 0.986079 3.65306 0.26756
SH032_HG514 31.85 1091.22 3199954870 3199868337 86533 3147873072 2309405851 146017640 442020433116 1293255740 0.002925783 138.0 39.5 283.8 142.4 98.4 0.7216995066558548 0.9999729580561241 1162.92 0.874268 0.00681258 0.989526 0.988402 0.987758 3.89966 0.204711
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