[Genome] SNP Strand and Contig Orientation

[Xueya Zhou]

Hello UCSC People,

I want to determine the exact genomic strand of certain SNPs. And I notice
that there is "strand" field in all SNP related tables in your genome
browser. But the meaning of this strand field is not quite clear to me.

I read through the makeDb documentation in kent source, and noticed that the
strand field in snp12x table is obtained from dbSNP ContigLoc table.
According to dbSNP documentation, the strand refers to the orientation of
SNPs relative to the contigs. So if I want to know the strand of a SNP on
certain genome assembly, I have to determine (1) which contig this SNP is
located on, AND (2) the orientation of that contig in the assembly. I think
ONLY if the contigs are all on the forward orientations as the chromosomes,
can we interpret the strand field as the genomic strand.

So I want to know if all the other SNP related tables inherit their the
strand fields from snp12x? And Can any one give me some idea about how many
strands on not on the forward orientation as the chromosomes on hg17 and
hg18 assembly?

Xueya