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Sample GSM2029877

Query DataSets for GSM2029877

Status

Public on Jul 14, 2016

Title

Kodi41 [GRC14300174]

Sample type

genomic

Source name

blood

Organism

Characteristics

population: Kodi
island: Sumba
country: Indonesia
region: Southeast Asia
gender: Male

Extracted molecule

genomic DNA

Extraction protocol

Extraction of genomic DNA from blood was performed using standard extraction protocols.

Label

biotin

Label protocol

Standard Illumina procedures.

Hybridization protocol

Standard Illumina procedures.

Scan protocol

Standard Illumina procedures.

Description

Genomic DNA extracted from blood was genotyped using Illumina HumanOmniExpress-24 v1.0 BeadChip platform.

Data processing

Illumina GenomeStudio Software has been used to analyze the data. GenomeStudio Genotyping Module Version is 1.9.4.
Genotype data is provided in each sample record.Dataset is also converted into PLINK format (http://pngu.mgh.harvard.edu/~purcell/plink/) . Files INDONESIA_SUMBA_TIMOR.bed INDONESIA_SUMBA_TIMOR.bim INDONESIA_SUMBA_TIMOR.fam are provided.

Submission date

Jan 07, 2016

Last update date

Jul 14, 2016

Contact name

Tatiana M. Karafet

E-mail(s)

tkarafet@email.arizona.edu

Phone

520-626-0404

Organization name

University of Arizona

Department

ARL

Lab

Michael Hammer's Research Group

Street address

BSW #246, 1041 E Lowell Str.

City

Tucson

State/province

AZ

ZIP/Postal code

85721

Country

USA

Platform ID

Series (1)

Small Traditional Human Communities Sustain Genomic Diversity Over Microgeographic Scales Despite Linguistic Isolation

Data table header descriptions
ID_REF	IlmnID
VALUE	Genotype: AA,AB,BB,or NC (no call)
Theta
R
B_Allele_Freq
GC_Score
Log_R_Ratio
Genotype

Data table
ID_REF	VALUE	Theta	R	B_Allele_Freq	GC_Score	Log_R_Ratio	Genotype
rs1000000-131_B_F_1894802339	BB	0.977	1.607	0.9976	0.7848	0.0977	GG
rs1000002-131_T_F_1889659641	AA	0.015	0.887	0.0000	0.8886	-0.2561	TT
rs10000023-131_B_F_1908645866	BB	0.982	1.772	1.0000	0.7886	0.1633	GG
rs1000003-131_B_R_1891325219	AA	0.041	1.174	0.0034	0.8833	-0.0863	AA
rs10000030-131_B_R_1891267789	BB	0.898	0.525	0.8988	0.6574	-0.0633	GG
rs10000037-131_B_R_1891342139	BB	0.983	0.956	1.0000	0.9440	-0.0875	GG
rs10000041-131_T_R_1893970874	AA	0.039	1.180	0.0045	0.9184	-0.0554	TT
rs10000042-131_T_R_1895028553	AB	0.617	1.089	0.5367	0.4109	0.0277	TC
rs10000049-131_T_F_1893954592	AA	0.034	1.416	0.0000	0.4231	0.2099	AA
rs1000007-131_T_F_1891267790	AA	0.015	0.943	0.0000	0.9357	-0.1302	TT
rs10000073-131_T_R_1895048370	AA	0.013	0.785	0.0000	0.7458	-0.0001	TT
rs10000081-131_B_F_1895064663	AA	0.042	0.905	0.0023	0.8981	-0.1545	TT
rs10000092-131_T_R_1911627639	AB	0.409	0.725	0.3988	0.8759	0.0031	TC
rs10000105-131_T_F_1893943453	BB	0.974	1.132	1.0000	0.8824	0.1059	GG
rs10000119-131_T_R_1893947293	BB	0.944	1.207	0.9774	0.8588	-0.0211	CC
rs10000124-131_B_R_1908800786	BB	0.974	1.508	1.0000	0.8140	0.1046	CC
rs10000154-131_T_F_1893949661	BB	0.972	0.940	1.0000	0.9142	-0.0075	GG
rs1000016-131_B_R_1891268428	AB	0.421	1.619	0.4622	0.8444	-0.1316	AG
rs10000160-131_T_F_1895138379	BB	0.956	1.157	1.0000	0.8523	-0.0195	GG
rs10000169-131_T_R_1891213580	AB	0.594	0.927	0.5306	0.9260	-0.1639	TC

Total number of rows: 716503

Table truncated, full table size 47922 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM2029877_9465554138_R03C02_Grn.idat.gz	4.7 Mb	(ftp)(http)	IDAT
GSM2029877_9465554138_R03C02_Red.idat.gz	4.8 Mb	(ftp)(http)	IDAT
Processed data included within Sample table
Processed data are available on Series record

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