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Status
Public on Dec 31, 2020
Title
Blood, BMI-Y144
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
5964706015-R01C02-1-Y144
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
0.9790373
1.162714
0.9920737
-0.05042822
ALGA0000014
BB
0.8145218
0.9821846
0.6664907
1
-0.04073125
ALGA0000021
BB
0.9480368
0.9811357
1.002095
1
-0.09553342
ALGA0000022
AA
0.868265
0.02646571
0.773525
0.000679593
-0.7103193
ALGA0000046
AA
0.916555
0.02747498
1.269728
0
0.04474213
ALGA0000047
BB
0.9032862
0.9486546
0.5279279
0.9828674
0.04711259
ALGA0000087
NC
0
0.9789325
1.278998
0.9915628
-1.069004
ALGA0000112
AA
0.7716642
0.04155245
0.532415
0.01334858
-0.3770805
ALGA0000120
AA
0.8562791
0.04670583
1.143498
0.06330696
-0.1673843
ALGA0000131
AA
0.9518364
0.02043771
1.10262
0
0.1439086
ALGA0000133
AA
0.8528799
0.01113139
1.576109
0
0.1748631
ALGA0000134
AA
0.8617834
0.000630089
1.657485
0
0.02590312
ALGA0000172
AA
0.9490964
0.009111976
1.304257
0
0.1886611
ALGA0000188
AA
0.840633
0.05002437
1.238516
0
-0.02138161
ALGA0000195
AA
0.704823
0.0179778
2.007071
0
-0.002993969
ALGA0000218
BB
0.8448049
0.9644611
1.359716
0.9860752
-0.0586767
ALGA0000232
AA
0.9600575
0.02282674
1.155632
0.005609987
-0.00738212
ALGA0000251
BB
0.8726248
0.9934399
1.100794
1
-0.04807938
ALGA0000269
BB
0.7406444
0.9698521
1.71303
1
-0.1124874
ALGA0000277
AA
0.8527849
0.01072653
1.35212
0
-0.2856993
62163 3698 Kbytes .Supplementary file Size Download File type/resource GSM4781285_5964706015_R01C02_Grn.idat.gz
454.9 Kb
(ftp) (http) IDAT
GSM4781285_5964706015_R01C02_Red.idat.gz
454.9 Kb
(ftp) (http) IDAT
Processed data included within Sample table
