基因芯片中TOP/BOT Strand and A/B Allele的区别
“TOP/BOT” Strand and “A/B” Allele
Rather than referencing the evolving public databases to provide accurate SNP strand and orientation, Illumina has developed a method to consistently designate SNPs based on the actual or contextual sequence of each individual SNP.The advantage of this method is that it will consistently designate the same SNP orientation and allele calls even if public SNP databases and genome assemblies change. This will enable researchers worldwide to easily correlate the genotype calls made today to research that may have been completed several years ago. 
A in Candidate allele: TOP
T in Candidate allele: BOT
sequence walking
If the SNP is an A/T] or a [C/G], then the above rules do not apply.  
To designate Strand, when the A or T in the first unambiguous pair is on the 5’ side of the SNP, then the sequence is designated TOP. When the A or T in the first unambiguous pair is on the 3’ side of the SNP, then the sequence is designated BOT.
To designate Allele for an [A/T] SNP, when the Strand is TOP then Allele A = A and Allele B = T. When the Strand is BOT, then Allele A = T and Allele B =A.
To designate Allele for a [C/G] SNP, when the Strand is TOP then Allele A = C and Allele B = G. When the Strand is BOT then Allele A = G and Allele B = C.
