File Info
- Filename
- control_metrics.csv
- Full Path
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/3e37ffd53e76a8c9c8bc1f56dcc3d2/control_metrics.csv
- Size
- 8.3 KB
- Attempt
Content
View in new tab| control_type | sample_id | variant_type | qc_metric_name | qc_value |
| germline | HCC1395_BL | cnv | germline_control_cnv_abnormal_ploidy | false |
| germline | HCC1395_BL | cnv | germline_control_cnv_abnormal_ploidy_chromosomes | NONE |
| germline | HCC1395_BL | cnv | germline_control_cnv_del_dup_pass_ratio | NA |
| germline | HCC1395_BL | cnv | germline_control_cnv_del_pass_count | 1 |
| germline | HCC1395_BL | cnv | germline_control_cnv_dup_pass_count | 0 |
| germline | HCC1395_BL | cnv | germline_control_cnv_landmark_del_missed | UGT2B17;UGT2B28 |
| germline | HCC1395_BL | cnv | germline_control_cnv_landmark_del_recovered_count | 0 |
| germline | HCC1395_BL | cnv | germline_control_cnv_landmark_del_truth_total | 2 |
| germline | HCC1395_BL | cnv | germline_control_cnv_qc_failed | false |
| germline | HCC1395_BL | cnv | germline_control_cnv_ugt2b17_del_cn | NA |
| germline | HCC1395_BL | cnv | germline_control_cnv_ugt2b17_del_filter | NOT_CALLED |
| germline | HCC1395_BL | cnv | germline_control_cnv_ugt2b28_del_cn | NA |
| germline | HCC1395_BL | cnv | germline_control_cnv_ugt2b28_del_filter | NOT_CALLED |
| germline | HCC1395_BL | snv_indel | germline_control_snv_indel_giab_missed_variants | chr11:78079607:T:C;chr12:14928963:A:C;chr13:101721213:A:T;chr14:20060200:G:T;chr19:14799626:C:T;chr19:43848513:T:C;chr2:184937028:A:G;chr4:122894207:T:C;chr4:168448702:A:T;chr5:120686124:G:A;chr7:102934552:TGAA:T;chr9:94606867:C:T |
| germline | HCC1395_BL | snv_indel | germline_control_snv_indel_giab_recovered_count | 0 |
| germline | HCC1395_BL | snv_indel | germline_control_snv_indel_giab_truth_total | 12 |
| germline | HCC1395_BL | snv_indel | germline_control_snv_indel_indel_count | 14 |
| germline | HCC1395_BL | snv_indel | germline_control_snv_indel_snv_count | 312 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_abnormal_ploidy | false |
| germline | Sig_18_Blood | cnv | germline_control_cnv_abnormal_ploidy_chromosomes | NONE |
| germline | Sig_18_Blood | cnv | germline_control_cnv_del_dup_pass_ratio | 3.0000 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_del_pass_count | 3 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_dup_pass_count | 1 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_landmark_del_missed | UGT2B17;UGT2B28 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_landmark_del_recovered_count | 0 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_landmark_del_truth_total | 2 |
| germline | Sig_18_Blood | cnv | germline_control_cnv_qc_failed | false |
| germline | Sig_18_Blood | cnv | germline_control_cnv_ugt2b17_del_cn | NA |
| germline | Sig_18_Blood | cnv | germline_control_cnv_ugt2b17_del_filter | NOT_CALLED |
| germline | Sig_18_Blood | cnv | germline_control_cnv_ugt2b28_del_cn | NA |
| germline | Sig_18_Blood | cnv | germline_control_cnv_ugt2b28_del_filter | NOT_CALLED |
| germline | Sig_18_Blood | snv_indel | germline_control_snv_indel_giab_missed_variants | chr11:78079607:T:C;chr12:14928963:A:C;chr13:101721213:A:T;chr14:20060200:G:T;chr19:14799626:C:T;chr19:43848513:T:C;chr2:184937028:A:G;chr4:122894207:T:C;chr4:168448702:A:T;chr5:120686124:G:A;chr7:102934552:TGAA:T;chr9:94606867:C:T |
| germline | Sig_18_Blood | snv_indel | germline_control_snv_indel_giab_recovered_count | 0 |
| germline | Sig_18_Blood | snv_indel | germline_control_snv_indel_giab_truth_total | 12 |
| germline | Sig_18_Blood | snv_indel | germline_control_snv_indel_indel_count | 18 |
| germline | Sig_18_Blood | snv_indel | germline_control_snv_indel_snv_count | 336 |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_lci | NA |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_max_msi_score | NA |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_mean_msi_score | NA |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_min_msi_score | NA |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_msi_status | NA |
| negative_somatic | HCC1395_BL | mimsi | negative_somatic_control_mimsi_uci | NA |
| negative_somatic | HCC1395_BL | msi | negative_somatic_control_msi_total_sites | 0 |
| negative_somatic | HCC1395_BL | msi | negative_somatic_control_msi_unstable_pct | 0.00 |
| negative_somatic | HCC1395_BL | msi | negative_somatic_control_msi_unstable_sites | 0 |
| negative_somatic | HCC1395_BL | snv_indel | negative_somatic_control_snv_indel_indel_count | 0 |
| negative_somatic | HCC1395_BL | snv_indel | negative_somatic_control_snv_indel_snv_count | 0 |
| negative_somatic | HCC1395_BL | tmb | negative_somatic_control_tmb_effective_coding_region_size | 34.15 |
| negative_somatic | HCC1395_BL | tmb | negative_somatic_control_tmb_non_synonymous_count | 0 |
| negative_somatic | HCC1395_BL | tmb | negative_somatic_control_tmb_score | 0.0 |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_lci | NA |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_max_msi_score | NA |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_mean_msi_score | NA |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_min_msi_score | NA |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_msi_status | NA |
| negative_somatic | Sig_18_Blood | mimsi | negative_somatic_control_mimsi_uci | NA |
| negative_somatic | Sig_18_Blood | msi | negative_somatic_control_msi_total_sites | 0 |
| negative_somatic | Sig_18_Blood | msi | negative_somatic_control_msi_unstable_pct | 0.00 |
| negative_somatic | Sig_18_Blood | msi | negative_somatic_control_msi_unstable_sites | 0 |
| negative_somatic | Sig_18_Blood | snv_indel | negative_somatic_control_snv_indel_indel_count | 0 |
| negative_somatic | Sig_18_Blood | snv_indel | negative_somatic_control_snv_indel_snv_count | 0 |
| negative_somatic | Sig_18_Blood | tmb | negative_somatic_control_tmb_effective_coding_region_size | 34.15 |
| negative_somatic | Sig_18_Blood | tmb | negative_somatic_control_tmb_non_synonymous_count | 0 |
| negative_somatic | Sig_18_Blood | tmb | negative_somatic_control_tmb_score | 0.0 |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_lci | NA |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_max_msi_score | NA |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_mean_msi_score | NA |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_min_msi_score | NA |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_msi_status | NA |
| positive_somatic | HCC1395_tumor | mimsi | positive_somatic_control_mimsi_uci | NA |
| positive_somatic | HCC1395_tumor | msi | positive_somatic_control_msi_total_sites | 0 |
| positive_somatic | HCC1395_tumor | msi | positive_somatic_control_msi_unstable_pct | 0.00 |
| positive_somatic | HCC1395_tumor | msi | positive_somatic_control_msi_unstable_sites | 0 |
| positive_somatic | HCC1395_tumor | snv_indel | positive_somatic_control_snv_indel_coa_missed_variants | 13655;163343;177678;13983;376002 |
| positive_somatic | HCC1395_tumor | snv_indel | positive_somatic_control_snv_indel_coa_recovered_count | 0 |
| positive_somatic | HCC1395_tumor | snv_indel | positive_somatic_control_snv_indel_coa_truth_total | 5 |
| positive_somatic | HCC1395_tumor | snv_indel | positive_somatic_control_snv_indel_indel_count | 0 |
| positive_somatic | HCC1395_tumor | snv_indel | positive_somatic_control_snv_indel_snv_count | 0 |
| positive_somatic | HCC1395_tumor | tmb | positive_somatic_control_tmb_effective_coding_region_size | 34.15 |
| positive_somatic | HCC1395_tumor | tmb | positive_somatic_control_tmb_non_synonymous_count | 0 |
| positive_somatic | HCC1395_tumor | tmb | positive_somatic_control_tmb_score | 0.0 |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_lci | NA |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_max_msi_score | NA |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_mean_msi_score | NA |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_min_msi_score | NA |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_msi_status | NA |
| positive_somatic | Sig_18_tissue | mimsi | positive_somatic_control_mimsi_uci | NA |
| positive_somatic | Sig_18_tissue | msi | positive_somatic_control_msi_total_sites | 0 |
| positive_somatic | Sig_18_tissue | msi | positive_somatic_control_msi_unstable_pct | 0.00 |
| positive_somatic | Sig_18_tissue | msi | positive_somatic_control_msi_unstable_sites | 0 |
| positive_somatic | Sig_18_tissue | snv_indel | positive_somatic_control_snv_indel_coa_missed_variants | 13655;163343;177678;13983;376002 |
| positive_somatic | Sig_18_tissue | snv_indel | positive_somatic_control_snv_indel_coa_recovered_count | 0 |
| positive_somatic | Sig_18_tissue | snv_indel | positive_somatic_control_snv_indel_coa_truth_total | 5 |
| positive_somatic | Sig_18_tissue | snv_indel | positive_somatic_control_snv_indel_indel_count | 0 |
| positive_somatic | Sig_18_tissue | snv_indel | positive_somatic_control_snv_indel_snv_count | 0 |
| positive_somatic | Sig_18_tissue | tmb | positive_somatic_control_tmb_effective_coding_region_size | 34.15 |
| positive_somatic | Sig_18_tissue | tmb | positive_somatic_control_tmb_non_synonymous_count | 0 |
| positive_somatic | Sig_18_tissue | tmb | positive_somatic_control_tmb_score | 0.0 |
99 rows