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The filters you have selected from various query interfaces will be stored here, in the 'Filter Cart'. The database will be queried using filters added to your 'Filter Cart', when multiple filters are defined, each will be executed using 'AND' logic, so with each filter that is applied the result set gets smaller.

From the 'Filter Cart' you can inspect each of the filters that have been defined, and you also have the option to remove filters. The 'Filter Cart' itself will display the number of filters applied along with the number of subjects that are identified by the combination of those filters. For example a GUID filter with two subjects, followed by a GUID filter for just one of those subjects would return only data for the subject that is in both GUID filters.

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Description
Value Range
Notes
Data Structures with shared data
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NGS QA

omics_qa

01

Next-gen sequencing data files QA

Download Definition as
Download Submission Template as
Element NameData TypeSizeRequiredConditionDescriptionValue RangeNotes
subjectkeyGUIDRequiredThe NDAR Global Unique Identifier (GUID) for research subjectNDAR*
src_subject_idString20RequiredSubject ID how it's defined in lab/project
interview_dateDateRequiredDate on which the interview/genetic test/sampling/imaging was completed. MM/DD/YYYYRequired field
interview_ageIntegerRequiredAge in months at the time of the interview/test/sampling/imaging.0 :: 1260Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
genderString20RequiredSex of the subjectM;FM = Male; F = Female
file_sourceString1,024RequiredFile name/location
omics_qa_01_idIntegerRequiredUnique ID for OMICS_QA_01 Structure
experiment_idIntegerRequiredID for the Experiment/settings/run
qplot_verString50RecommendedQPLOT Software version
qplot_p1FloatConditionalnotNull(qplot_ver)QPLOT:Total Reads (e6)
qplot_p2FloatConditionalnotNull(qplot_ver)QPLOT:MappingRate (%)
qplot_p3FloatConditionalnotNull(qplot_ver)QPLOT:MapRate_MQpass (%)
qplot_p4FloatConditionalnotNull(qplot_ver)QPLOT:TargetMapping (%)
qplot_p5FloatConditionalnotNull(qplot_ver)QPLOT:ZeroMapQual (%)
qplot_p6FloatConditionalnotNull(qplot_ver)QPLOT:MapQual<10*%)
qplot_p7FloatConditionalnotNull(qplot_ver)QPLOT:PairedReads (%)
qplot_p8FloatConditionalnotNull(qplot_ver)QPLOT:ProperPaired (%)
qplot_p9FloatConditionalnotNull(qplot_ver)QPLOT:MappedBases (%)
qplot_p10FloatConditionalnotNull(qplot_ver)QPLOT:Q20Bases (%)
qplot_p11FloatConditionalnotNull(qplot_ver)QPLOT:Q20BasesPct (%)
qplot_p12FloatConditionalnotNull(qplot_ver)QPLOT:MeanDepth
qplot_p13FloatConditionalnotNull(qplot_ver)QPLOT:GenomeCover (%)
qplot_p14FloatConditionalnotNull(qplot_ver)QPLOT:EPS_MSE
qplot_p15FloatConditionalnotNull(qplot_ver)QPLOT:EPS_Cycle_Mean
qplot_p16FloatConditionalnotNull(qplot_ver)QPLOT:GCBiasMSE
qplot_p17FloatConditionalnotNull(qplot_ver)QPLOT:ISize_mode
qplot_p18FloatConditionalnotNull(qplot_ver)QPLOT:ISize_medium
qplot_p19FloatConditionalnotNull(qplot_ver)QPLOT:DupRate(%)
qplot_p20FloatConditionalnotNull(qplot_ver)QPLOT:QCFailRate(%)
qplot_p21FloatConditionalnotNull(qplot_ver)QPLOT:BaseComp_A(%)
qplot_p22FloatConditionalnotNull(qplot_ver)QPLOT:BaseComp_C(%)
qplot_p23FloatConditionalnotNull(qplot_ver)QPLOT:BaseComp_G(%)
qplot_p24FloatConditionalnotNull(qplot_ver)QPLOT:BaseComp_T(%)
qplot_p25FloatConditionalnotNull(qplot_ver)QPLOT:BaseComp_O(%)
picard_verString50RecommendedPICARD Software version
picard_p1String20ConditionalnotNull(picard_ver)PICARD:Library
picard_p2FloatConditionalnotNull(picard_ver)PICARD:Unpaired_Reads_Examined
picard_p3FloatConditionalnotNull(picard_ver)PICARD:Read_Pairs_Examined
picard_p4FloatConditionalnotNull(picard_ver)PICARD:Unmapped_Reads
picard_p5FloatConditionalnotNull(picard_ver)PICARD:Unpaired_Read_Duplicates
picard_p6FloatConditionalnotNull(picard_ver)PICARD:Read_Pair_Duplicates
picard_p7FloatConditionalnotNull(picard_ver)PICARD:Read_Pair_Optical_Duplicates
picard_p8FloatConditionalnotNull(picard_ver)PICARD:Percent_Duplication
picard_p9FloatConditionalnotNull(picard_ver)PICARD:Estimated_Libarary_Size
samtools_verString50Recommendedsamtools version
samtools_p1FloatConditionalnotNull(samtools_ver)FlagStat(samtools): in total (QC-Passed + QC Failed)
samtools_p2FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Duplicates
samtools_p3FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Mapped
samtools_p4FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Paired
samtools_p5FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Read1
samtools_p6FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Read2
samtools_p7FloatConditionalnotNull(samtools_ver)FlagStat(samtools):Properly paired
samtools_p8FloatConditionalnotNull(samtools_ver)FlagStat(samtools):with itself and mate mapped
samtools_p9FloatConditionalnotNull(samtools_ver)FlagStat(samtools):singletons
samtools_p10FloatConditionalnotNull(samtools_ver)FlagStat(samtools):with mate mapped to a different chr
samtools_p11FloatConditionalnotNull(samtools_ver)FlagStat(samtools):with mate mapped to a different chr (mapQ>=5)
samtools_p12FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr1, sequence length
samtools_p13FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr1, mapped reads
samtools_p14FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr1, unmapped reads
samtools_p15FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr2, sequence length
samtools_p16FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr2, mapped reads
samtools_p17FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr2, unmapped reads
samtools_p18FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr3, sequence length
samtools_p19FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr3, mapped reads
samtools_p20FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr3, unmapped reads
samtools_p21FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr4, sequence length
samtools_p22FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr4, mapped reads
samtools_p23FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr4, unmapped reads
samtools_p24FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr5, sequence length
samtools_p25FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr5, mapped reads
samtools_p26FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr5, unmapped reads
samtools_p27FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr6, sequence length
samtools_p28FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr6, mapped reads
samtools_p29FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr6, unmapped reads
samtools_p30FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr7, sequence length
samtools_p31FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr7, mapped reads
samtools_p32FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr7, unmapped reads
samtools_p33FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr8, sequence length
samtools_p34FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr8, mapped reads
samtools_p35FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr8, unmapped reads
samtools_p36FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr9, sequence length
samtools_p37FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr9, mapped reads
samtools_p38FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr9, unmapped reads
samtools_p39FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr10, sequence length
samtools_p40FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr10, mapped reads
samtools_p41FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr10, unmapped reads
samtools_p42FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr11, sequence length
samtools_p43FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr11, mapped reads
samtools_p44FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr11, unmapped reads
samtools_p45FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr12, sequence length
samtools_p46FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr12, mapped reads
samtools_p47FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr12, unmapped reads
samtools_p48FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr13, sequence length
samtools_p49FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr13, mapped reads
samtools_p50FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr13, unmapped reads
samtools_p51FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr14, sequence length
samtools_p52FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr14, mapped reads
samtools_p53FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr14, unmapped reads
samtools_p54FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr15, sequence length
samtools_p55FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr15, mapped reads
samtools_p56FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr15, unmapped reads
samtools_p57FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr16, sequence length
samtools_p58FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr16, mapped reads
samtools_p59FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr16, unmapped reads
samtools_p60FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr17, sequence length
samtools_p61FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr17, mapped reads
samtools_p62FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr17, unmapped reads
samtools_p63FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr18, sequence length
samtools_p64FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr18, mapped reads
samtools_p65FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr18, unmapped reads
samtools_p66FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr19, sequence length
samtools_p67FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr19, mapped reads
samtools_p68FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr19, unmapped reads
samtools_p69FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr20, sequence length
samtools_p70FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr20, mapped reads
samtools_p71FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr20, unmapped reads
samtools_p72FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr21, sequence length
samtools_p73FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr21, mapped reads
samtools_p74FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr21, unmapped reads
samtools_p75FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr22, sequence length
samtools_p76FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr22, mapped reads
samtools_p77FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: Chr22, unmapped reads
samtools_p78FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrX, sequence length
samtools_p79FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrX, mapped reads
samtools_p80FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrX, unmapped reads
samtools_p81FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrY, sequence length
samtools_p82FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrY, mapped reads
samtools_p83FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrY, unmapped reads
samtools_p84FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference Sequence: ChrMT, sequence length
samtools_p85FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrMT, mapped reads
samtools_p86FloatConditionalnotNull(samtools_ver)idxstats(samtools):Reference: ChrMT, unmapped reads
samtools_p87FloatConditionalnotNull(samtools_ver)idxstats(samtools):Unmapped *:, sequence length
samtools_p88FloatConditionalnotNull(samtools_ver)idxstats(samtools):Unmapped: *, mapped reads
samtools_p89FloatConditionalnotNull(samtools_ver)idxstats(samtools):Unmapped: *, unmapped reads
sanders_snp_fingerprintString1,024RecommendedSanders SNP-Fingerprint
qc_file1FileRequiredLocation of QA file
qc_file1_typeString100RequiredFile Type
qc_file2FileRecommendedLocation of QA file
qc_file2_typeString100ConditionalnotNull(qc_file2)File Type
qc_file3FileRecommendedLocation of QA file
qc_file3_typeString100ConditionalnotNull(qc_file3)File Type
qc_file4FileRecommendedLocation of QA file
qc_file4_typeString100ConditionalnotNull(qc_file4)File Type
origin_dataset_idIntegerRecommendedOrigin dataset Id
job_nameString50RecommendedIdentity of the run for pipeline processes
Data Structure

This page displays the data structure defined for the measure identified in the title and structure short name. The table below displays a list of data elements in this structure (also called variables) and the following information:

  • Element Name: This is the standard element name
  • Data Type: Which type of data this element is, e.g. String, Float, File location.
  • Size: If applicable, the character limit of this element
  • Required: This column displays whether the element is Required for valid submissions, Recommended for valid submissions, Conditional on other elements, or Optional
  • Description: A basic description
  • Value Range: Which values can appear validly in this element (case sensitive for strings)
  • Notes: Expanded description or notes on coding of values
  • Aliases: A list of currently supported Aliases (alternate element names)
  • For valid elements with shared data, on the far left is a Filter button you can use to view a summary of shared data for that element and apply a query filter to your Cart based on selected value ranges

At the top of this page you can also:

  • Use the search bar to filter the elements displayed. This will not filter on the Size of Required columns
  • Download a copy of this definition in CSV format
  • Download a blank CSV submission template prepopulated with the correct structure header rows ready to fill with subject records and upload

Please email the The NDA Help Desk with any questions.

Distribution for DataStructure: omics_qa01 and Element:
Chart Help

Filters enable researchers to view the data shared in NDA before applying for access or for selecting specific data for download or NDA Study assignment. For those with access to NDA shared data, you may select specific values to be included by selecting an individual bar chart item or by selecting a range of values (e.g. interview_age) using the "Add Range" button. Note that not all elements have appropriately distinct values like comments and subjectkey and are not available for filtering. Additionally, item level detail is not always provided by the research community as indicated by the number of null values given.

Filters for multiple data elements within a structure are supported. Selections across multiple data structures will be supported in a future version of NDA.