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NIMH Data Archive
NDA ABCD CCF OAI NIAAADA AMP SCZ HEAL

NGS QA

0 Shared Subjects

Next-gen sequencing data files QA
Omics
Evaluated Data
02/14/2014
omics_qa01
04/18/2023
View Change History
01
Definition
Submission Template
Query Element Name Data Type Size Required Condition Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR*
src_subject_id String 20 Required Subject ID how it's defined in lab/project
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_age Integer Required Age in months at the time of the interview/test/sampling/imaging. 0::1440 Age 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.
sex String 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported gender
file_source String 1,024 Required File name/location
Query omics_qa_01_id Integer Required Unique ID for OMICS_QA_01 Structure
Query experiment_id Integer Required ID for the Experiment/settings/run
qplot_ver String 50 Recommended QPLOT Software version
Query qplot_p1 Float Conditional notNull(qplot_ver) QPLOT:Total Reads (e6)
Query qplot_p2 Float Conditional notNull(qplot_ver) QPLOT:MappingRate (%)
Query qplot_p3 Float Conditional notNull(qplot_ver) QPLOT:MapRate_MQpass (%)
Query qplot_p4 Float Conditional notNull(qplot_ver) QPLOT:TargetMapping (%)
Query qplot_p5 Float Conditional notNull(qplot_ver) QPLOT:ZeroMapQual (%)
Query qplot_p6 Float Conditional notNull(qplot_ver) QPLOT:MapQual<10*%)
Query qplot_p7 Float Conditional notNull(qplot_ver) QPLOT:PairedReads (%)
Query qplot_p8 Float Conditional notNull(qplot_ver) QPLOT:ProperPaired (%)
Query qplot_p9 Float Conditional notNull(qplot_ver) QPLOT:MappedBases (%)
Query qplot_p10 Float Conditional notNull(qplot_ver) QPLOT:Q20Bases (%)
Query qplot_p11 Float Conditional notNull(qplot_ver) QPLOT:Q20BasesPct (%)
Query qplot_p12 Float Conditional notNull(qplot_ver) QPLOT:MeanDepth
Query qplot_p13 Float Conditional notNull(qplot_ver) QPLOT:GenomeCover (%)
Query qplot_p14 Float Conditional notNull(qplot_ver) QPLOT:EPS_MSE
Query qplot_p15 Float Conditional notNull(qplot_ver) QPLOT:EPS_Cycle_Mean
Query qplot_p16 Float Conditional notNull(qplot_ver) QPLOT:GCBiasMSE
Query qplot_p17 Float Conditional notNull(qplot_ver) QPLOT:ISize_mode
Query qplot_p18 Float Conditional notNull(qplot_ver) QPLOT:ISize_medium
Query qplot_p19 Float Conditional notNull(qplot_ver) QPLOT:DupRate(%)
Query qplot_p20 Float Conditional notNull(qplot_ver) QPLOT:QCFailRate(%)
Query qplot_p21 Float Conditional notNull(qplot_ver) QPLOT:BaseComp_A(%)
Query qplot_p22 Float Conditional notNull(qplot_ver) QPLOT:BaseComp_C(%)
Query qplot_p23 Float Conditional notNull(qplot_ver) QPLOT:BaseComp_G(%)
Query qplot_p24 Float Conditional notNull(qplot_ver) QPLOT:BaseComp_T(%)
Query qplot_p25 Float Conditional notNull(qplot_ver) QPLOT:BaseComp_O(%)
picard_ver String 50 Recommended PICARD Software version
picard_p1 String 20 Conditional notNull(picard_ver) PICARD:Library
Query picard_p2 Float Conditional notNull(picard_ver) PICARD:Unpaired_Reads_Examined
Query picard_p3 Float Conditional notNull(picard_ver) PICARD:Read_Pairs_Examined
Query picard_p4 Float Conditional notNull(picard_ver) PICARD:Unmapped_Reads
Query picard_p5 Float Conditional notNull(picard_ver) PICARD:Unpaired_Read_Duplicates
Query picard_p6 Float Conditional notNull(picard_ver) PICARD:Read_Pair_Duplicates
Query picard_p7 Float Conditional notNull(picard_ver) PICARD:Read_Pair_Optical_Duplicates
Query picard_p8 Float Conditional notNull(picard_ver) PICARD:Percent_Duplication
Query picard_p9 Float Conditional notNull(picard_ver) PICARD:Estimated_Libarary_Size
samtools_ver String 50 Recommended samtools version
Query samtools_p1 Float Conditional notNull(samtools_ver) FlagStat(samtools): in total (QC-Passed + QC Failed)
Query samtools_p2 Float Conditional notNull(samtools_ver) FlagStat(samtools):Duplicates
Query samtools_p3 Float Conditional notNull(samtools_ver) FlagStat(samtools):Mapped
Query samtools_p4 Float Conditional notNull(samtools_ver) FlagStat(samtools):Paired
Query samtools_p5 Float Conditional notNull(samtools_ver) FlagStat(samtools):Read1
Query samtools_p6 Float Conditional notNull(samtools_ver) FlagStat(samtools):Read2
Query samtools_p7 Float Conditional notNull(samtools_ver) FlagStat(samtools):Properly paired
Query samtools_p8 Float Conditional notNull(samtools_ver) FlagStat(samtools):with itself and mate mapped
Query samtools_p9 Float Conditional notNull(samtools_ver) FlagStat(samtools):singletons
Query samtools_p10 Float Conditional notNull(samtools_ver) FlagStat(samtools):with mate mapped to a different chr
Query samtools_p11 Float Conditional notNull(samtools_ver) FlagStat(samtools):with mate mapped to a different chr (mapQ>=5)
Query samtools_p12 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr1, sequence length
Query samtools_p13 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr1, mapped reads
Query samtools_p14 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr1, unmapped reads
Query samtools_p15 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr2, sequence length
Query samtools_p16 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr2, mapped reads
Query samtools_p17 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr2, unmapped reads
Query samtools_p18 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr3, sequence length
Query samtools_p19 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr3, mapped reads
Query samtools_p20 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr3, unmapped reads
Query samtools_p21 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr4, sequence length
Query samtools_p22 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr4, mapped reads
Query samtools_p23 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr4, unmapped reads
Query samtools_p24 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr5, sequence length
Query samtools_p25 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr5, mapped reads
Query samtools_p26 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr5, unmapped reads
Query samtools_p27 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr6, sequence length
Query samtools_p28 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr6, mapped reads
Query samtools_p29 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr6, unmapped reads
Query samtools_p30 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr7, sequence length
Query samtools_p31 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr7, mapped reads
Query samtools_p32 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr7, unmapped reads
Query samtools_p33 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr8, sequence length
Query samtools_p34 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr8, mapped reads
Query samtools_p35 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr8, unmapped reads
Query samtools_p36 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr9, sequence length
Query samtools_p37 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr9, mapped reads
Query samtools_p38 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr9, unmapped reads
Query samtools_p39 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr10, sequence length
Query samtools_p40 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr10, mapped reads
Query samtools_p41 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr10, unmapped reads
Query samtools_p42 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr11, sequence length
Query samtools_p43 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr11, mapped reads
Query samtools_p44 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr11, unmapped reads
Query samtools_p45 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr12, sequence length
Query samtools_p46 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr12, mapped reads
Query samtools_p47 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr12, unmapped reads
Query samtools_p48 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr13, sequence length
Query samtools_p49 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr13, mapped reads
Query samtools_p50 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr13, unmapped reads
Query samtools_p51 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr14, sequence length
Query samtools_p52 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr14, mapped reads
Query samtools_p53 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr14, unmapped reads
Query samtools_p54 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr15, sequence length
Query samtools_p55 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr15, mapped reads
Query samtools_p56 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr15, unmapped reads
Query samtools_p57 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr16, sequence length
Query samtools_p58 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr16, mapped reads
Query samtools_p59 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr16, unmapped reads
Query samtools_p60 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr17, sequence length
Query samtools_p61 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr17, mapped reads
Query samtools_p62 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr17, unmapped reads
Query samtools_p63 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr18, sequence length
Query samtools_p64 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr18, mapped reads
Query samtools_p65 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr18, unmapped reads
Query samtools_p66 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr19, sequence length
Query samtools_p67 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr19, mapped reads
Query samtools_p68 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr19, unmapped reads
Query samtools_p69 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr20, sequence length
Query samtools_p70 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr20, mapped reads
Query samtools_p71 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr20, unmapped reads
Query samtools_p72 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr21, sequence length
Query samtools_p73 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr21, mapped reads
Query samtools_p74 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr21, unmapped reads
Query samtools_p75 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr22, sequence length
Query samtools_p76 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr22, mapped reads
Query samtools_p77 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: Chr22, unmapped reads
Query samtools_p78 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrX, sequence length
Query samtools_p79 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrX, mapped reads
Query samtools_p80 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrX, unmapped reads
Query samtools_p81 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrY, sequence length
Query samtools_p82 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrY, mapped reads
Query samtools_p83 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrY, unmapped reads
Query samtools_p84 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference Sequence: ChrMT, sequence length
Query samtools_p85 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrMT, mapped reads
Query samtools_p86 Float Conditional notNull(samtools_ver) idxstats(samtools):Reference: ChrMT, unmapped reads
Query samtools_p87 Float Conditional notNull(samtools_ver) idxstats(samtools):Unmapped *:, sequence length
Query samtools_p88 Float Conditional notNull(samtools_ver) idxstats(samtools):Unmapped: *, mapped reads
Query samtools_p89 Float Conditional notNull(samtools_ver) idxstats(samtools):Unmapped: *, unmapped reads
sanders_snp_fingerprint String 1,024 Recommended Sanders SNP-Fingerprint
qc_file1 File Required Location of QA file
qc_file1_type String 100 Required File Type
qc_file2 File Recommended Location of QA file
qc_file2_type String 100 Conditional notNull(qc_file2) File Type
qc_file3 File Recommended Location of QA file
qc_file3_type String 100 Conditional notNull(qc_file3) File Type
qc_file4 File Recommended Location of QA file
qc_file4_type String 100 Conditional notNull(qc_file4) File Type
Query origin_dataset_id Integer Recommended Origin dataset Id
Query job_name String 50 Recommended Identity 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

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