VCF File Headings

The chromosome of the reference genome. Chromosomes appear in the same order as the reference FASTA file.

The single-base position of the variant in the reference chromosome.
For SNPs, this position is the reference base with the variant; for indels or deletions, this position is the reference base immediately before the variant.

The rs number for the SNP obtained from dbSNP.txt, if applicable.
If there are multiple rs numbers at this location, the list is semicolon delimited. If no dbSNP entry exists at this position, a missing value marker ('.') is used.

The reference genotype. For example, a deletion of a single T is represented as reference TT and alternate T. An A to T single nucleotide variant is represented as reference A and alternate T.

The alleles that differ from the reference read.
For example, an insertion of a single T is represented as reference A and alternate AT. An A to T single nucleotide variant is represented as reference A and alternate T.

A Phred-scaled quality score assigned by the variant caller.
Higher scores indicate higher confidence in the variant and lower probability of errors. For a quality score of Q, the estimated probability of an error is 10^-(Q/10). For example, the set of Q30 calls has a 0.1% error rate. Many variant callers assign quality scores based on their statistical models, which are high in relation to the error rate observed.