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Status
Public on Dec 31, 2020
Title
Blood, BMI-Y432
Sample type
genomic
Source name
blood
Organism
Sus scrofa Characteristics
tissue: blood
Treatment protocol
No treatment
Extracted molecule
genomic DNA
Extraction protocol
Classic method of phenol-chloroform
Label
biotin
Label protocol
biotin
Hybridization protocol
The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50-mers (covalently linked to one of up to 300,000 bead types) during hybridization.
Scan protocol
The BeadChip was scanned using iScan system produced by Illumina Inc.
Description
5964706050-R03C01-23-Y432
Data processing
BeadStudio (Illumina Inc.) software were used to genotype the SNPs.
Submission date
Sep 14, 2020
Last update date
Dec 31, 2020
Contact name
Jinlong Huo
E-mail(s)
jinlonghuo973@gmail.com Phone
086 13708761403
Organization name
Yunnan Agricultural University
Department
Faculty of Animal Science and Technology
Lab
Huo
Street address
Jin-hei
City
Kunming
State/province
Yunnan
ZIP/Postal code
650201
Country
China
Platform ID
GPL11379 Series (2)
GSE157934 Analysis of Whole Genome Sequence and Genome-wide SNPs in Highly Inbred Pigs [Array]
GSE157935 Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line
Data table header descriptions ID_REF VALUE Genotype calls (we use the genotyped nucleotides (A, T, C, G) of the two alleles, or no value (no call))
GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
Data table ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio ALGA0000009
BB
0.8486087
0.9882967
1.104602
1
-0.1154462
ALGA0000014
BB
0.8145218
0.9827014
0.6702322
1
-0.03175922
ALGA0000021
BB
0.9480368
0.9805997
0.9855577
1
-0.1200362
ALGA0000022
AA
0.8621675
0.02842635
0.7224441
0.002619054
-0.8101161
ALGA0000046
AA
0.916555
0.02182127
1.279147
0
0.06018218
ALGA0000047
BB
0.9032862
0.9404451
0.4330865
0.9735125
-0.2412342
ALGA0000087
NC
0
0.9795438
1.277584
0.99218
-1.0706
ALGA0000112
AA
0.7716642
0.04569864
0.5209542
0.01730052
-0.4115938
ALGA0000120
AA
0.9101826
0.03794879
1.191699
0.05314742
-0.1038432
ALGA0000131
AA
0.9518364
0.01748534
1.021845
0
0.03624288
ALGA0000133
AA
0.8528799
0.009517691
1.594309
0
0.192783
ALGA0000134
AA
0.8617834
0.004512215
1.677569
0
0.03994281
ALGA0000172
AA
0.9490964
0.007904777
1.305474
0
0.1911065
ALGA0000188
AA
0.840633
0.04579281
1.204792
0
-0.05952231
ALGA0000195
AA
0.704823
0.01806885
1.997105
0
-0.01025402
ALGA0000218
BB
0.8448049
0.9584758
1.386912
0.9801378
-0.03686367
ALGA0000232
AA
0.9600575
0.01988542
1.169857
0.002422394
0.01220952
ALGA0000251
BB
0.8726248
0.992991
1.074907
1
-0.08295167
ALGA0000269
BB
0.7406444
0.9705255
1.738471
1
-0.09039042
ALGA0000277
AA
0.8527849
0.01006455
1.411796
0
-0.222931
62163 3670 Kbytes .Supplementary file Size Download File type/resource GSM4781276_5964706050_R03C01_Grn.idat.gz
458.7 Kb
(ftp) (http) IDAT
GSM4781276_5964706050_R03C01_Red.idat.gz
454.8 Kb
(ftp) (http) IDAT
Processed data included within Sample table
