Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing datase
as well as genotype-phenotype associations. Numerous databases of human genomics and bioinformatics have been developed, including the UKbiobank6, Genome Aggregation Database7, 1000 Genomes project8, UK10K project9, ChinaMAP10, and NyuWa project11. Although many studies ...
and Hsu,Y.H. (2016) A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples. Sci. Rep., 10.1038/srep39313.
Validation Phased haplotype data for 80.6 kb region of chromosome 1 (between positions NC_000001.11: 159,203,314–159,283,887) was manually downloaded for all 2535 indi- viduals of the 1000GP panel (Phase 3; GRCh37) from the 1000 Genomes browser. After removing 31 related individuals...
Okamura K, Kawai T, Hata K, Nakabayashi K. Lists of HumanMethylation450 BeadChip probes with nucleotide-variant information obtained from the Phase 3 data of the 1000 Genomes Project. Genom Data. 2016;7:67-9.Okamura K, Kawai T, Hata K, Nakabayashi K. Lists of HumanMethylation450 BeadChip ...
genotype was based on dosage (probability > 0.9) imputed using the 1000 Genomes Phase I reference panel and filtered by the following criteria: HWE < 1 × 10−6, individual missingness >5 %, SNP missingness >5 %, and MAF < 0.0005 (~3 ...
We performed imputation for Twins UK study subjects based on 1000 Genomes data as described previously.13 This involved estimating the phase of contiguous variants in the subjects using the haplotypes calculated from the 1000 Genomes Project consisting of 1094 individuals and 2188 haplotypes and the ...
The MAF of each SNV is a global MAF calculated with respect to 1,092 samples from Phase 1 of the 1000 Genomes Project3. Analysis of ASB SNVs found in TF motifs. We obtain a list of all TF motifs and their corresponding PWMs from Kheradpour and Kellis69 (http://compbio.mit. edu/...
1000GP phase 1 low-coverage sequence data. We downloaded the GLs for 1,092 1000GP samples from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/ 20110521/. This data set contains GLs for 36,820,992 SNPs, 1,384,273 short bi- allelic indels and 14,017 SVs. The GLs for SNPs were...
Our estimated thresholds were DISCUSSION In the present study, we estimated the empirical genome-wide significance thresholds for the five ancestral populations based on the GWAS simulations conducted using the 1000 Genomes Project Phase 3 data set. The results suggested that, for non-African ...