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Status
Public on Dec 31, 2020
Title
Blood, BMI-Y229
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-R02C01-22-Y229
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
0.9866843
1.098928
0.9999366
-0.1244393
ALGA0000014
BB
0.8145218
0.9775897
0.6869317
1
-0.005090628
ALGA0000021
AB
0.9480368
0.4651282
1.331546
0.4508521
-0.0388637
ALGA0000022
AA
0.8682662
0.02517849
0.9100715
0
-0.4749762
ALGA0000046
AA
0.916555
0.02857857
1.312483
0
0.09159034
ALGA0000047
BB
0.9032862
0.9439016
0.498466
0.9774513
-0.03727438
ALGA0000087
NC
0
0.9801536
1.312527
0.9927957
-1.031671
ALGA0000112
AA
0.7716642
0.05309936
0.537465
0.02435452
-0.3721293
ALGA0000120
AA
0.8924018
0.04209008
1.179104
0.05795196
-0.1210537
ALGA0000131
AA
0.9518364
0.01986917
1.056428
0
0.08257073
ALGA0000133
AA
0.8528799
0.008574133
1.554796
0
0.1573708
ALGA0000134
AA
0.8617834
0.003316573
1.680708
0
0.04366681
ALGA0000172
AA
0.9490964
0.007688436
1.302267
0
0.1877557
ALGA0000188
AA
0.840633
0.05196562
1.229268
0
-0.03296772
ALGA0000195
AA
0.704823
0.01759362
1.987152
0
-0.01705124
ALGA0000218
BB
0.8448049
0.9548123
1.412434
0.9765037
-0.01467746
ALGA0000232
AA
0.9600575
0.02256244
1.207463
0.005323552
0.05608861
ALGA0000251
BB
0.8726248
0.9916288
1.073201
1
-0.08687703
ALGA0000269
BB
0.7406444
0.9756264
1.7619
1
-0.06478548
ALGA0000277
AA
0.8527849
0.009356478
1.395864
0
-0.2388113
62163 3670 Kbytes .Supplementary file Size Download File type/resource GSM4781274_5964706050_R02C01_Grn.idat.gz
457.5 Kb
(ftp) (http) IDAT
GSM4781274_5964706050_R02C01_Red.idat.gz
454.7 Kb
(ftp) (http) IDAT
Processed data included within Sample table
