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refsnp

Question tag: refsnp 26 Questions

0 Votes 1 Ans

How do I code a URL so that a refSNP (rs) number can be linked directly to the genotype and allele frequency report?

Allele code directly Frequency genotype linked refsnp Rs URL

0 Votes 1 Ans

Why does the integrated maps section of the rs9288952 refSNP report show the alleles to be A/G, but the Geneview section shows them to be C/T?

alleles geneview Integrated Maps refsnp report section shows

0 Votes 1 Ans

In the “Integrated Maps” section of rs55956772, it appears that each assembly maps the refSNP to different chromosomes without overlap. Is this due to small flanking sequence?

appears assembly chromosomes different Maps refsnp section

0 Votes 1 Ans

Will refSNP flanks change orientation between builds?

builds flanks Orientation refsnp

0 Votes 1 Ans

Minor Allele Frequency (MAF) found in the population diversity section of the refSNP report is very high in SNPs from different sets of samples from the same ethnicity. Why?

different Diversity high MAF minor allele frequency population refsnp report section SNPs

0 Votes 1 Ans

How is HWP (Hardy Weinberg Probability) found in the Population Diversity section of the refSNP report determined, and how does it relate to genotype data?

Diversity hardy weinberg hwp population probability refsnp relate report section

0 Votes 1 Ans

The refSNP report for rs2037101 shows this variation has a frequency of zero. Does this mean that this polymorphism is not confirmed by population data?

Frequency mean polymorphism refsnp report shows variation Zero

0 Votes 1 Ans

I’ve submitted millions of mouse SNPs, and have their submitted (ss) numbers — how do I check to see if they have refSNP (rs) numbers yet?

I’ve mouse Numbers refsnp Rs SNPs SS submitted

0 Votes 1 Ans

Do you have a key for the refSNP cluster report FASTA section that would help me decipher the sequence colors and the information above the sequence?

cluster colors decipher fasta help key refsnp report section sequence

0 Votes 1 Ans

Which tables and columns in the schema contain the data found in the Population Diversity section of the refSNP Cluster Report?

cluster columns contain Data Diversity population refsnp schema section tables

0 Votes 1 Ans

Why do maps associated with refSNP cluster reports, exclude regulatory sequences?

associated cluster EXCLUDE Maps refsnp regulatory reports sequences

0 Votes 1 Ans

How do I download the data located in the Population Diversity section of the refSNP report for all human SNPs? Would I get it on your FTP site?

Data Diversity download Human located population refsnp report section SNPs

0 Votes 1 Ans

A refSNP report shows 90 individuals were sampled for genotype data. Is 90 the total number of individuals contributing chromosomes for the assay sample size and the population data sample size?

Data genotype individuals refsnp report sampled shows total

0 Votes 1 Ans

The “Source” column in the Population Diversity section of the refSNP cluster report contains the abbreviations IG, AF, and GF. What do these abbreviations stand for?

cluster column Diversity population refsnp report section

0 Votes 1 Ans

The refSNP report for rs17362 shows the two genotypes for this refSNP listed simply as “A” and “C”. Why do these genotypes look like this rather than the typical “C/C”, “A/A”, “A/C”?

genotypes refsnp report shows

0 Votes 1 Ans

What is the meaning of the symbols that represent validation status in the RefSNP cluster report?

cluster refsnp report Status Symbols validation

0 Votes 1 Ans

How do I access the legend for the icons in the SNP validation section of the refSNP (rs) and submitted SNP (ss) reports?

icons legend refsnp Rs section SNP SS submitted validation

0 Votes 1 Ans

What does N/N represent in refSNP sequence?

refsnp sequence

0 Votes 1 Ans

On the refSNP page, where do I find information about amino acid changes resulting from the variation?

amino acid changes page refsnp variation

0 Votes 1 Ans

Are there any refSNP fields that indicate which SNP allele matches the reference genome sequence upon which the SNP was mapped?

Allele Fields genome indicate mapped Reference refsnp sequence SNP