| 5prime3prime_bias |
|
| additional_details |
modifier of a term where the additional details are not supported/available a... |
| additional_family_members_with_variant |
List of related participant IDs carrying the same variant |
| additional_modifiers |
|
| affected_status |
Indicate affected status of individual (overall with respect to primary pheno... |
| age_at_collection |
age or participant in years at biosample collection |
| age_at_enrollment |
age in years at which consent was originally obtained |
| age_at_last_observation |
Age at last observation, aka age in years at the last time the center can vou... |
| aligned_atac_short_read_file |
name and path of file with aligned reads |
| aligned_atac_short_read_id |
identifier for aligned ATAC-seq data |
| aligned_atac_short_read_index_file |
name and path of index file corresponding to aligned reads file |
| aligned_dna_short_read_file |
name and path of file with aligned reads |
| aligned_dna_short_read_id |
|
| aligned_dna_short_read_index_file |
name and path of index file corresponding to aligned reads file |
| aligned_dna_short_read_set_id |
identifier for experiment set |
| aligned_file |
|
| aligned_id |
table_name |
| aligned_index_file |
|
| aligned_nanopore_file |
name and path of file with aligned reads |
| aligned_nanopore_id |
|
| aligned_nanopore_index_file |
name and path of index file corresponding to aligned reads file |
| aligned_nanopore_set_id |
identifier for experiment set |
| aligned_pac_bio_file |
name and path of file with aligned reads |
| aligned_pac_bio_id |
|
| aligned_pac_bio_index_file |
name and path of index file corresponding to aligned reads file |
| aligned_pac_bio_set_id |
identifier for experiment set |
| aligned_read_length_mean |
Mean length of aligned reads |
| aligned_rna_short_read_file |
name and path of file with aligned reads |
| aligned_rna_short_read_id |
identifier for aligned_short_read (primary key) |
| aligned_rna_short_read_index_file |
name and path of index file corresponding to aligned reads file |
| alignment_log_file |
path of (log) file with all parameters for alignment software |
| alignment_postprocessing |
If any post processing was applied |
| alignment_software |
Software including version number |
| allele_balance_or_heteroplasmy_percentage |
Reported allele balance (mosaic) or heteroplasmy percentage (mitochondrial) |
| alt |
Alternate position of the variant |
| analysis_details |
brief description of the analysis pipeline used for producing the asc_file; p... |
| analyte_id |
|
| analyte_processing_details |
details about how the analyte or original biosample was extracted or processe... |
| analyte_type |
analyte derived from the primary_biosample |
| ancestry_detail |
Additional specific ancestry description free text beyond what is captured by... |
| application_kit |
Library prep kits for special applications |
| asc_atac_short_read_id |
unique key for table (anvil requirement) |
| asc_file |
name and path of the tsv file with allele-specific chromatin accessibility me... |
| asc_md5sum |
md5 checksum for called_peaks_file |
| barcode_kit |
Barcode kit used |
| by_strand |
run reports separate reads per strand |
| called_peaks_atac_short_read_id |
identifier for called peaks |
| called_peaks_file |
name and path of the bed file with open chromatin peaks after QC filtering |
| called_variants_dna_file |
name and path of the file with variant calls |
| called_variants_dna_short_read_id |
unique key for table (anvil requirement) |
| called_variants_nanopore_id |
unique key for table (anvil requirement) |
| called_variants_pac_bio_id |
unique key for table (anvil requirement) |
| caller_software |
variant calling software used including version number |
| chemistry_type |
chemistry type used for the experiment |
| chrom |
Chromosome of the variant |
| chrom_end |
End position chromosome of SV |
| ClinGen_allele_ID |
ClinGen Allele ID for cross table refrence |
| condition_id |
MONDO/OMIM number for condition used for variant interpretation |
| condition_inheritance |
Description of the expected inheritance of condition used for variant interpr... |
| consanguinity |
Indicate if consanguinity is present or suspected within a family |
| consanguinity_detail |
Free text description of any additional consanguinity details |
| consent_code |
Consent group pertaining to this participant's data |
| contamination |
Contamination level estimate |
| copy_number |
CNV copy number |
| date_data_generation |
Date of data generation (First sequencing date) |
| estimated_library_size |
|
| experiment_atac_short_read_id |
identifier for experiment |
| experiment_dna_short_read_id |
identifier for experiment |
| experiment_id |
table_name |
| experiment_nanopore_id |
identifier for experiment |
| experiment_pac_bio_id |
identifier for experiment |
| experiment_rna_short_read_id |
identifier for experiment |
| experiment_sample_id |
identifier used in the data file (e |
| experiment_type |
|
| family_history_detail |
Details about family history that do not fit into structured fields |
| family_id |
Identifier for family (primary key) |
| fragmentation_method |
method used for shearing/fragmentation |
| gene_annotation |
annotation file used for alignment |
| gene_annotation_details |
|
| gene_disease_validity |
Validity assessment of the gene-disease relationship |
| gene_known_for_phenotype |
Indicate if the gene listed is a candidate or known disease gene |
| gene_of_interest |
HGNC approved symbol of the known or candidate gene(s) that are relevant for ... |
| genetic_findings_id |
Unique ID of this variant in this participant (primary key) |
| genome_coverage |
e |
| gregor_center |
GREGoR Center to which the participant is originally associated |
| GREGoR_ClinVar_SCV |
ClinVar accession number for the variant curation submitted by your center |
| GREGoR_variant_classification |
Clinical significance of variant described to condition listed as determined ... |
| het_sites_file |
VCF file containing prefiltered heterozygous sites used for reference alignme... |
| het_sites_md5sum |
md5 checksum for het_sites_file |
| hgvs |
genomic HGVS description of the variant |
| hgvsc |
HGVS c |
| hgvsp |
HGVS p |
| hours_since_last_meal |
his is relevant when analyzing metabolomics data |
| id_in_table |
|
| includes_CpG_methylation |
run reports CpG methylation |
| includes_kinetics |
run reports base kinetics |
| instrument_ics_version |
Version number of PacBio instrument control software |
| internal_project_id |
An identifier used by GREGoR research centers to identify a set of participan... |
| known_condition_name |
Free text of condition name |
| library_prep_type |
type of library prep |
| library_size |
library prep - expected size of library from FemtoPulse |
| linked_variant |
Second variant in recessive cases |
| linked_variant_phase |
|
| mapped_reads_pct |
Number between 1 and 100, na |
| maternal_id |
participant_id for mother; 0 if not available |
| md5sum |
md5 checksum for file |
| mean_coverage |
Mean coverage of either the genome or the targeted regions |
| method_of_discovery |
The method/assay(s) used to identify the candidate |
| methylation_called |
Indicates whether 5mC methylation has been called and annotated in the BAM fi... |
| missing_variant_case |
Indication of whether this is known to be a missing variant case, see notes f... |
| missing_variant_details |
For missing variant cases, indicate gene(s) or region of interest and reason ... |
| movie_length_hours |
sequencing - length of sequencing collection, in hrs |
| movie_name |
sequencing - unique name of sequencing collection |
| notes |
Free text field to explain edge cases or discovery updates or list parallel e... |
| num_aligned_bases |
Number of bases in aligned reads |
| num_aligned_reads |
Total aligned reads |
| num_bases |
Number of bases (before/ignoring alignment) |
| num_reads |
Total reads (before/ignoring alignment) |
| onset_age_range |
|
| ontology |
|
| partial_contribution_explained |
List of specific phenotypes (HPO IDs) explained by the condition associated w... |
| participant_drugs_intake |
The list of drugs patient is on, at the time of sample collection |
| participant_id |
|
| participant_special_diet |
If the patient was fasting, when the sample was collected |
| passage_number |
passage_number is relevant for fibroblast cultures and possibly iPSC |
| paternal_id |
participant_id for father; 0 if not available |
| peak_caller_software |
peak calling software used including version number |
| peak_set_type |
peak set type, according to ENCODE descriptors |
| peaks_md5sum |
md5 checksum for called_peaks_file |
| pedigree_file |
name of file (renamed from pedigree_image because it can contain a PED file o... |
| pedigree_file_detail |
Free text description of other family structure/pedigree file caption or lege... |
| percent_chrX_Y |
|
| percent_GC |
|
| percent_Globin |
|
| percent_mRNA |
|
| percent_mtRNA |
|
| percent_multimapped |
how many reads aligned to multiple places |
| percent_rRNA |
|
| percent_UMI |
|
| percent_unaligned |
how many reads didn't align |
| percent_uniquely_aligned |
how many reads aligned to just one place |
| phenotype_contribution |
Contribution of variant-linked condition to participant's phenotype |
| phenotype_description |
human-readable 'Phenotypic one-line summary' for why this individual is of in... |
| phenotype_id |
primary key |
| pmid_id |
Case specific PubMed ID if applicable |
| polymerase_kit |
sequencing - part number of polymerase kit used |
| pos |
Start position of the variant |
| pos_end |
End position of SV |
| presence |
|
| primary_biosample |
Tissue type of biosample taken from the participant that the analyte was extr... |
| primary_biosample_details |
Free text to capture information not in structured fields |
| primary_biosample_id |
Optional ID for the biosample; allows for linking of multiple analytes extrac... |
| prior_testing |
Text description of any genetic testing for individual conducted prior to enr... |
| proband_relationship |
Text description of individual relationship to proband in family, especially ... |
| proband_relationship_detail |
Other proband relationship not captured in enumeration above |
| public_database_ID_other |
Public database variant/case ID |
| public_database_other |
Public databases that this variant in this participant has been submitted by ... |
| quality_issues |
describe if there are any QC issues that would be important to note |
| read_error_rate |
Mean empirical per-base error rate of aligned reads |
| read_length |
sequenced read length (bp); GREGoR RCs do paired end sequencing, so is the ex... |
| read_length_mean |
Mean length of all reads (before/ignoring alignment) |
| recontactable |
Is the originating GREGoR Center likely able to recontact this participant |
| ref |
Reference allele of the variant |
| reference_assembly |
|
| reference_assembly_details |
|
| reference_assembly_uri |
|
| reported_ethnicity |
Self/submitter-reported ethnicity (OMB categories) |
| reported_race |
Self/submitter-reported race (OMB categories) |
| RIN |
RIN number for quality of sample |
| sample_transformation_detail |
details regarding sample transformation |
| seq_library_prep_kit_method |
Library prep kit used |
| sequencing_event_details |
describe if there are any sequencing-specific issues that would be important ... |
| sequencing_kit |
sequencing - part number of sequencing kit reagents |
| sequencing_platform |
sequencing platform used for the experiment |
| sex |
Biological sex assigned at birth (aligned with All of Us) |
| sex_concordance |
Comparison between reported sex vs genotype sex; Other if ploidy NOT XX or XY... |
| sex_detail |
Optional free-text field to describe known discrepancies between 'sex' value ... |
| single_or_paired_ends |
single or paired end |
| size_selection_method |
library prep - method use for library size selection |
| smrt_cell_id |
sequencing - unique serial number for SMRT Cell |
| smrt_cell_kit |
sequencing - part number of the SMRT Cell |
| smrtlink_server_version |
Version number of PacBio SMRTLink software |
| solve_status |
Indication of whether the submitting RC considers this case 'solved' |
| sv_type |
|
| syndromic |
For participants with few HPO terms, this optional field is to provide contex... |
| table_name |
|
| target_insert_size |
insert size the protocol targets for DNA fragments |
| targeted_region_bed_file |
name and path of bed file uploaded to workspace |
| targeted_regions_method |
Which capture kit is used |
| term_id |
|
| time_to_freeze |
time (in hours) from collection to freezing the sample |
| tissue_affected_status |
If applicable to disease (suspected mosaic), is the tissue from an affected s... |
| total_reads |
total number of reads |
| transcript |
Text description of transcript overlapping the variant |
| twin_id |
participant_id for twins, triplets, etc; 0 if not available |
| variant_inheritance |
Detection of variant in parents |
| variant_reference_assembly |
The genome build for identifying the variant position |
| variant_type |
|
| variant_types |
types of variants called |
| was_barcoded |
indicates whether samples were barcoded on this flowcell |
| within_site_batch_name |
batch number for the site, important for future batch correction |
| zygosity |
Zygosity of variant |