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Status
Public on Dec 31, 2020
Title
Blood, BMI-0308
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-R01C02-0403-0308
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
0.9854364
1.115553
0.9986535
-0.1039846
ALGA0000014
BB
0.8145218
0.9783813
0.703719
1
0.03110701
ALGA0000021
BB
0.9480368
0.9825137
1.023538
1
-0.06370992
ALGA0000022
AA
0.8678067
0.02365815
0.7599515
0
-0.73409
ALGA0000046
AA
0.916555
0.03221428
1.27741
0
0.04945108
ALGA0000047
BB
0.9032862
0.9422204
0.4790442
0.9755356
-0.09515557
ALGA0000087
NC
0
0.5634007
0.1210192
0.5720405
-4.470711
ALGA0000112
AA
0.7716642
0.04973528
0.4879731
0.02114805
-0.5089784
ALGA0000120
AA
0.8252828
0.04936753
1.398144
0.06639495
0.1214681
ALGA0000131
AA
0.9518364
0.02087768
0.9882744
0
-0.01435459
ALGA0000133
AA
0.8528799
0.008540193
1.508666
0
0.1139469
ALGA0000134
AA
0.8617834
0.004925767
1.662315
0
0.0264093
ALGA0000172
BB
0.9490964
0.9808754
1.222488
0.9901325
-0.02259691
ALGA0000188
AA
0.840633
0.05037218
1.251358
0
-0.006638042
ALGA0000195
AA
0.704823
0.01836813
2.029782
0
0.01290206
ALGA0000218
AA
0.8448049
0.01810102
1.528154
0
-0.03849387
ALGA0000232
AA
0.9600575
0.02109114
1.165516
0.003729068
0.0060502
ALGA0000251
BB
0.8726248
0.990513
1.090969
0.999456
-0.06452477
ALGA0000269
BB
0.7406444
0.9761187
1.753149
1
-0.07136073
ALGA0000277
BB
0.8527849
0.9874877
1.32597
1
-0.1313347
62163 3682 Kbytes .Supplementary file Size Download File type/resource GSM4781273_5964706050_R01C02_Grn.idat.gz
455.9 Kb
(ftp) (http) IDAT
GSM4781273_5964706050_R01C02_Red.idat.gz
453.5 Kb
(ftp) (http) IDAT
Processed data included within Sample table
