Variant Query

The authorized users are able to query SNP and INDEL data via gene symbol, rs ID, genomic region, or genomic position. The searching result table includes the information of chromosome name, position, rs ID in dbSNP v149, reference genotype, alteration genotype, variant quality, allele frequency in the ChinaMAP sample sets, gene symbol, affected transcript, and allele frequency in 1000 Genomes database.

Database

The following databases are open to query.

ChinaMAP.phase1

It contains the information of 136,745,826 SNPs and 10,703,115 INDELs on autosomes from phase 1 study of ChinaMAP. The phase 1 study proposes to analyze 10,588 whole genome sequencing data (~40X) in Chinese natural population.

The query result is shown in the figure below:

• Chr, Chromosome

• Position, The reference position

• dbSNP, The rs ID in dbSNP

• Ref, Reference base

• Alt, Alternate base

• Qual, Phred-scaled quality score for the assertion made in ALT

• Alt freq, Allele Frequency

• Count, Allele count in genotypes / Total number of alleles in called genotypes

• Gene, Gene symbol

• Transcript, Affected transcript

• 1KGP_AF, Allele Frequency in 1KGP (1000 Genomes Project)

• 1KGP_EAS_AF, Allele frequency of EAS populations in the 1KGP

• 1KGP_AMR_AF, Allele frequency of AMR populations in the 1KGP

• 1KGP_AFR_AF, Allele frequency of AFR populations in the 1KGP

• 1KGP_EUR_AF, Allele frequency of EUR populations in the 1KGP

• 1KGP_SAS_AF, Allele frequency of SAS populations in the 1KGP

The flowchart of Variants calling:

The genome build is GRCh38.