Which countries are involved in the international Hapmap project?
The project was a collaboration among researchers at academic centers, non-profit biomedical research groups and private companies in Japan, the United Kingdom, Canada, China, Nigeria and the United States. A list of participating and funding institutions is available at: http://hapmap.ncbi.nlm.nih.gov/groups.html.
What did the 1000 genome project discover?
Overall, the project discovered and characterized more than 88 million variants, including 84.7 million SNPs, 2.6 million short insertions/deletions (indels), and 60,000 structural variants, that were integrated into a high-quality haplotype scaffold.
How many human SNPs are there?
They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person’s genome. These variations may be unique or occur in many individuals; scientists have found more than 100 million SNPs in populations around the world.
What was the final phase of the 1000 Genomes Project?
In IGSR, data is organised into collections that roughly correspond to studies or projects. The samples collected by the 1000 Genomes Project have now been used in many different studies, some generating new data and others reanalysing existing data. The final phase of the 1000 Genomes Project was phase 3 and represents 2504 samples on GRCh37.
Are there 1000 Genomes Phase 3 structural variants?
1000 Genomes Phase 3 structural variants as reported in a companion paper specifically dedicated to SV analysis. Much of these data are identical to those reported in the main paper as study estd214. See Variant Summary counts for estd219 in dbVar Variant Summary.
How big is the 1000 Genomes data set?
The project now has data and variant genotypes for more than 1000 individuals in 14 populations. The ftp site contains more than 120Tbytes of data in 200,000 files. DATA TYPE FILE FORMAT SIZE sequence FASTQ 43 Tbases raw sequence alignment BAM 56 Tbytes of BAM files variants VCF 38.9M SNPs ~4.7M short indels Discoverability
Is the 1000 Genomes based on GRCh38 assembly?
An updated set of files showing the 1000 Genomes phase three variation calls on GRCh38 is now available. These files are based on dbSNP 149 and a “liftover” mapping from the GRCh37 genome assembly used by the 1000 Genomes Project to the newer GRCh38 assembly.