BnIR Brassica napus multi-omics information resource ————A multi-omics database with various tools for Brassica napus research and breeding
Vcf example

A01	124600	A01_124600_SNV	C	T	.	PASS	.	GT	0|0	1|1
A01	124713	A01_124713_SNV	T	G	.	PASS	.	GT	0|0	0|0
A01	124751	A01_124751_SNV	A	G	.	PASS	.	GT	0|0	1|1
A01	124781	A01_124781_SNV	A	G	.	PASS	.	GT	0|0	0|0
A01	124787	A01_124787_SNV	C	T	.	PASS	.	GT	0|0	1|1
A01	125023	A01_125023_SNV	G	A	.	PASS	.	GT	0|0	1|1
A01	125046	A01_125046_SNV	A	G	.	PASS	.	GT	0|0	1|1
A01	125144	A01_125144_SNV	G	A	.	PASS	.	GT	0|0	1|1
A01	125194	A01_125194_SNV	G	A	.	PASS	.	GT	0|0	1|1
A01	193368	A01_193368_SNV	G	GT	.	PASS	.	GT	1|1	0|0

The contig and genomic coordinates on which the variant occurs. Note that for deletions the position given is actually the base preceding the event.

An optional identifier for the variant. Based on the contig and position of the call and whether a record exists at this site in a reference database such as dbSNP. A typical identifier is the dbSNP ID, which in human data would look like rs28548431, for example.

The reference allele and alternative allele(s) observed in a sample, set of samples, or a population in general (depending how the VCF was generated). The REF and ALT alleles are the only required elements of a VCF record that tell us whether the variant is a SNP or an indel (or in complex cases, a mixed-type variant). If we look at the following two sites, we see the first is a SNP, the second is an insertion and the third is a deletion:
20  10001298    .   T   A   884.77  .   [CLIPPED]   GT:AD:DP:GQ:PL  1/1:0,30:30:89:913,89,0
20  10001436    .   A   AAGGCT  1222.73 .   [CLIPPED]   GT:AD:DP:GQ:PL  1/1:0,28:28:84:1260,84,0
20  10004769    .   TAAAACTATGC T   622.73  .   [CLIPPED]   GT:AD:DP:GQ:PL  0/1:18,17:35:99:660,0,704
Note that REF and ALT are always given on the forward strand. For insertions, the ALT allele includes the inserted sequence as well as the base preceding the insertion so you know where the insertion is compared to the reference sequence. For deletions, the ALT allele is the base before the deletion.

The Phred-scaled probability that a REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is -10 * log(1-p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in 10^10 chance (see the Technical Documentation). These values can grow very large when a large amount of data is used for variant calling, so QUAL is not often a very useful property for evaluating the quality of a variant call. See our documentation on filtering variants for more information on this topic.

Not to be confused with the sample-level annotation GQ; see this FAQ article for an explanation of the differences in what they mean and how they should be used.

This field contains the name(s) of any filter(s) that the variant fails to pass, or the value PASS if the variant passed all filters. If the FILTER value is ., then no filtering has been applied to the records. It is extremely important to apply appropriate filters before using a variant callset in downstream analysis. See our documentation on filtering variants for more information on this topic.

Various site-level annotations. This field is not required to be present in the VCF.

The annotations contained in the INFO field are represented as tag-value pairs, where the tag and value are separated by an equal sign, ie =, and pairs are separated by colons, ie ; as in this example: MQ=99.00;MQ0=0;QD=17.94. They typically summarize context information from the samples, but can also include information from other sources (e.g. population frequencies from a database resource). Some are annotated by default by the GATK tools that produce the callset, and some can be added on request. They are always defined in the VCF header, so that is an easy way to check what an annotation means if you do not recognize it. You can also find additional information on how they are calculated and how they should be interpreted in the Tool Index.

Sample-level annotations
At this point you have met all the fields up to INFO in this lineup:
#CHROM  POS ID  REF ALT     QUAL    FILTER  INFO    FORMAT  NA12878 [other samples...]
All the rest is going to be sample-level information. Sample-level annotations are tag-value pairs, like the INFO annotations, but the formatting is a bit different. The short names of the sample-level annotations are recorded in the FORMAT field. The annotation values are then recorded in corresponding order in each sample column (where the sample names are the SM tags identified in the read group data). Typically, you will at minimum have information about the genotype and confidence in the genotype for the sample at each site. See the next section on genotypes for more details.