MapSeq - Help - Comparing Genotyping Data

Main Concepts in MapSeq

Sample: A sample is a biological sample (e.g. a blood sample) submitted to the sequencing project. These samples undergo sequencing, followed by read mapping onto a reference genome, and genotyping at variable positions. In our documentation, sometimes samples are referred to as isolates.

Variable Position: A variable position is a genomic locus where significant nucleotide variation (e.g. SNP, indel, inversion, etc.) has been observed in one or more samples. Our catalogue of variable positions is derived from the analysis of variability in all sequenced samples. MapSeq currently only reports and analyze SNPs, but in the future will handle other types of variations.

Phenotypic Positions: MapSeq contains a catalogue of known phenotypic mutations, which are genomic variations that have been reported in the literature to be phenotypically significant.

Allele: A variable position is characterized by two or more alleles, which are the nucleotides that are likely to occur at that position.

Call: A call is the genotyping information for a sample at a given variable position. It reports which alleles are observed for that sample at that position. A call is made only if there is sufficient support (i.e. enough sequencing reads). For any given sample, the genotype may not necessarily be called at all positions.

Reads: The support for allele calls is derived from the number of reads (produced by sample sequencing) which are mapped at a given position. The mapping of reads is known as pileup data.

Metadata: A sample's public metadata is descriptive information that can be displayed to all users. It includes geographical location and contributor's details.

Study: Each sample is submitted by a study, which may have submitted several other samples for sequencing. Each study has one or more investigators who are registered users of MapSeq/pf, and who control metadata associated to the study's samples. All collaborators of a study can view the genotyping data for samples submitted by the study.