DB schema for genotype database

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Primary Data Tables

Sample
 subjectID VARCHAR(17) NOT NULL,       #KR-KR-000001-1-01
 providerID VARCHAR(10) NOT NULL,      #KR-CGS
 countryCode VARCHAR(2) NOT NULL,      #KR
 ethnicity VARCHAR(2) NOT NULL,        #KR
 gender CHAR(1) NULL,                  #M,F
 age INT NULL,                         #30
 chipID VARCHAR(15) NOT NULL,          #
 PRIMARY KEY(subjectID)                

Genotype
 probeID VARCHAR(13) NOT NULL,         #SNP_A-1650338
 dbSNPrsID VARCHAR(15) NULL,           #rs782
 subjectID VARCHAR(17) NOT NULL,       #KR-KR-000001-1-01
 genotype VARCHAR(6) NOT NULL,         #AA,AT,TT, NoCall
 confidence FLOAT NOT NULL,            #0.001465
 PRIMARY KEY(probeID)

AffySNPInfo
 probeID VARCHAR(13) NOT NULL,         #SNP_A-1650338
 dbSNPrsID VARCHAR(15) NULL,           #rs836702
 chromosome VARCHAR(5) NULL,           #chr2
 physicalPos INT NULL,                 #168550528
 tscID VARCHAR(15) NULL,               #TSC58722
 alleleA CHAR(1) NULL,                 #C
 alleleB CHAR(1) NULL,                 #G
 cytoBand VARCHAR(15) NULL,            #q24.3
 strand CHAR(1) NULL,                  #+
 downMSAT VARCHAR(255) NULL,           #ACCESSION:D2S2345; DISTANCE:4847; START:168545681; STOP:168546109
 upMSAT VARCHAR(255) NULL,             #ACCESSION:D2S2761; DISTANCE:34523; START:168585051; STOP:168585352
 flankSeq TEXT NULL,                   #ataagaattccccctcttcacatga[C/G]gtattttttttttttttttttaaca
 fragmentLen INT NULL,                 #715
 decodeAvg FLOAT NULL,                 #172.6467556
 marshfieldAvg FLOAT NULL,             #171.0498161
 slm1Avg FLOAT NULL,                   #162.6906085
 freqAAfAm FLOAT NULL,                 #0.634
 freqAAsian FLOAT NULL,                #0.464
 freqACauc FLOAT NULL,                 #0.868
 hetAfAm FLOAT NULL,                   #0.464
 hetAsian FLOAT NULL,                  #0.497
 hetCauc FLOAT NULL,                   #0.229
 overlapMSAT VARCHAR(255) NULL,        #ACCESSION:D7S631; DISTANCE:0; START:133397157; STOP:133908452
 upstreamGene TEXT NULL,               #Title:Homo sapiens UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase,
 downstreamGene TEXT NULL,             #Title:Homo sapiens UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase,
 PRIMARY KEY(probeID)

Provider
 providerID VARCHAR(10) NOT NULL,      #KR-CGS
 contactName VARCHAR(30) NULL,         #KilDong Hong
 contactEmail VARCHAR(30) NULL,        <a href="mailto:#kdHong@kribb.re.kr">#kdHong@kribb.re.kr</a>
 contactPhone VARCHAR(30) NULL,        #82-2-380-xxxx
 institution VARCHAR(255) NULL,        #KNIH
 institutionUrl VARCHAR(255) NULL,     #http://nih.go.kr/
 address VARCHAR(255) NULL,            #Seoul, Korea
 postalCode VARCHAR(20) NULL,          #122-701
 PRIMARY KEY(providerID)

Secondary Data Tables

GenotypeFull*                          #GenotypeFullKR
 probeID VARCHAR(13) NOT NULL,         #SNP_A-1650338
 dbSNPrsID VARCHAR(15) NULL,           #rs836702
 alleles CHAR(3) NOT NULL,             #C/G
 chromosome VARCHAR(5) NULL,           #chr2
 physicalPos INT NULL,                 #168550528
 cytoBand VARCHAR(15) NULL,            #q24.3
 strand CHAR(1) NULL,                  #+
 providerID VARCHAR(10) NOT NULL,      #KR-CGS
 QCValue CHAR(3) NOT NULL,             #QC+
 subjectID_01 CHAR(2) NOT NULL,        #CC (field name) KR-KR-000001-1-01
 subjectID_02 CHAR(2) NOT NULL,        #CC (field name) KR-KR-000002-1-01
 subjectID_03 CHAR(2) NOT NULL,        #NN (field name) KR-KR-000003-1-01
 subjectID_04 CHAR(2) NOT NULL,        #CG (field name) KR-KR-000004-1-01
     ...
 subjectID_90 CHAR(2) NOT NULL,        #GG (field name) KR-KR-000090-1-01

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