Variation and Sequence data.

Amino acid / cDNA transcript / RNA variation.

Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC).

Reference identifier for cDNA transcript/protein, with version, from NCBI's RefSeq or ENSEMBL. This reference sequence identifier must match the type in the Sequence.type field.

Quantity of the sequence.

The coordinate of the variant.

The chromosome containing the genetic finding. The value set will be 1-22, X, Y when the species is human without chromosome abnormality. Otherwise, NCBI-Gene code system should be used.

Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strand.

Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strand.

The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.

The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.

Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.

Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand.

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here .

Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.

0-based start position (inclusive) of the sequence.

0-based end position (exclusive) of the sequence.

Quality score.

Platform.

The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.

Allele frequencies.

Values: amplificaiton / deletion / LOH.

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

Information of chip.

Chip id.

Chip manufacturer id.

Chip version.

External repository.

URI of a GA4GH repository which contains further details about the genetics data.

URI of a GA4GH repository which contains further details about the genetics data.

URI of the page containing information about the structure of the repository.

Id of the GA4GH call set that matches identity of patient. A CallSet in GA4GH represents an individual.

Id of the GA4GH read group from which details about the sequence can be found. A read group in GA4GH represents a set of DNA reads processed the same way by the sequencer.