Skills

Genome, lost genes (pLoF mutations) SNP,INDEL

Genome, clinical annotations (only pathogenic and protective clinvar mutations) SNP,INDEL

chr: chromosome; position: position in chromosome (using Hg38 coordinates); dbsnpid: id of variant (mutation); found: this variant found in so many genomes in this database; who: max 10 genomes with this variant from this database sorted by similarity; freq: (max) frequency of this variant in public databases; homozygous: variant in both copies of the genome; gene: gene name; effect and description: description from clinvar database; note: variants with high frequency in public (freq) or this database; comment: Clinical annotations will change a lot in the future! Annotation of lost genes may not change.

Circo

The outer concentric ring is chromosomal information; The second ring represents the read coverage in histogram style. A histogram is the average coverage of a 0.5Mbp region; The third ring represents indel density in scatter style. A black dot is calculated as indel number in a range of 1Mbp/1Mbp); The fourth ring represents snp density in scatter style. A green dot is calculated as snp number in a range of 1Mbp/1Mbp); The fifth ring represents the proportion of homozygous SNP (orange) and heterozygous SNP (grey) in histogram style. A histogram is calculated from a 1Mbp region; The sixth ring represents the CNV inference. Red means gain, and green means loss; The most central ring represents the SV inference in exonic and splicing regions. If SV is called using breakdancer or crest, then CTX (orange), INS (green), DEL (grey), ITX (pink) and INV (blue). If SV is called using delly, then TRA (orange), INS (green), DEL (grey), DUP (pink) and INV (blue);

Similar genomes (max total of 3704046 used for caculating match%)

who: maximum 20 most similar genomes in this database sorted by number of common SNP variants; match: number of common SNP variants; total: total number of SNP variants in similar genome; match: similarity = (common variants)/min(total variants in tested or similar genome);

Statistics