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Sample GSM2443854

Query DataSets for GSM2443854

Status

Public on Jan 04, 2020

Title

Botlikh1033

Sample type

genomic

Source name

cheek swab

Organism

Characteristics

population: Botlikh
village: Botlikh
region: Daghestan
gender: Male

Extracted molecule

genomic DNA

Extraction protocol

Extraction of genomic DNA from cheek swab 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 cheek swab 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.

Submission date

Jan 04, 2017

Last update date

Jan 04, 2020

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)

Genetic variation in four highland populations in the context of broader genetic diversity in Daghestan.

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	0.973	1.570	0.9937	0.7942	-0.0047	GG
rs1000002-131_T_F_1889659641	BB	0.964	0.932	0.9903	0.8844	0.0116	CC
rs10000023-131_B_F_1908645866	AA	0.019	1.819	0.0000	0.8082	-0.1941	TT
rs1000003-131_B_R_1891325219	AA	0.045	1.917	0.0000	0.7431	-0.0706	AA
rs10000030-131_B_R_1891267789	BB	0.984	0.691	1.0000	0.8397	0.0558	GG
rs10000037-131_B_R_1891342139	BB	0.961	1.117	1.0000	0.9088	0.1218	GG
rs10000041-131_T_R_1893970874	AB	0.494	1.097	0.5179	0.9066	-0.2507	TG
rs10000042-131_T_R_1895028553	AB	0.671	1.027	0.5840	0.7871	-0.0207	TC
rs10000049-131_T_F_1893954592	AA	0.035	1.339	0.0000	0.4568	0.1149	AA
rs1000007-131_T_F_1891267790	AA	0.022	0.892	0.0000	0.8475	-0.1026	TT
rs10000073-131_T_R_1895048370	AA	0.024	1.107	0.0000	0.8805	0.1575	TT
rs10000081-131_B_F_1895064663	AA	0.034	0.899	0.0000	0.8697	-0.1448	TT
rs10000092-131_T_R_1911627639	AB	0.398	0.879	0.4169	0.8353	0.1451	TC
rs10000105-131_T_F_1893943453	BB	0.981	1.119	1.0000	0.4874	0.0884	GG
rs10000119-131_T_R_1893947293	BB	0.962	1.245	0.9976	0.8404	-0.0018	CC
rs10000124-131_B_R_1908800786	BB	0.962	1.465	0.9905	0.8184	-0.0658	CC
rs10000154-131_T_F_1893949661	AB	0.567	1.045	0.5359	0.9105	-0.0254	AG
rs1000016-131_B_R_1891268428	AB	0.458	1.616	0.4828	0.8294	-0.0874	AG
rs10000160-131_T_F_1895138379	BB	0.964	0.780	1.0000	0.7876	-0.6246	GG
rs10000169-131_T_R_1891213580	AB	0.566	1.182	0.4824	0.9043	0.2370	TC

Total number of rows: 708595

Table truncated, full table size 47479 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM2443854_200644210084_R06C01_Grn.idat.gz	5.0 Mb	(ftp)(http)	IDAT
GSM2443854_200644210084_R06C01_Red.idat.gz	5.1 Mb	(ftp)(http)	IDAT
Processed data provided as supplementary file
Processed data are available on Series record

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