|
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 |
|
|
|