Does Ensembl report variation alleles on the forward strand or reverse strand?
In views like the variation tab, the majority of alleles are reported on the forward strand. For example A/T in this view signifies that A is the forward stranded allele on the reference genome, and T is the alternate allele (also on the forward strand). Most of our SNPs and short insertion-deletions are from NCBI dbSNP. From dbSNP 2.0 (Build 152) variants are reported only in the forward strand. But variants from earlier releases can be on either strand. Ensembl determines the forward-stranded allele and reports it. On displays where variants are shown as part of a gene sequence, the alleles are shown as they are in the cDNA or gene. For example, if it is a reverse-stranded gene, you will see the allele on the reverse strand in the gene and transcript sequences.
There are a few minor exceptions. When a variant has multiple mappings to the genome, and at least one of those is to the reverse strand, then we will report the alleles on their original strand. Also, for species where the data has been imported long time ago, the alleles will still match the original submitted strand (it can be the reverse strand) as received from dbSNP.
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