Download LD2SNPing v2.0 User Manual

LD2SNPing User Manual
4.3.2. Sample file input for the tutorial of LD calculation/visualization
These sample files provide the chance for users to practice the LD2SNPing software.
The SNP is defined by the nucleotide variant (allele) larger than 1% (Minimal allele
frequency; MAF > 0.01) of the population. Therefore, for those allele frequencies less
than 1% is not shown in the 2D-LD plot in default setting, such as the SNP1, 3, 5-9,
11-13, 15, 19, 22-26, 28, 30 and 32 of sample 4 in Fig. 15A. Those SNPs with MAF
<0.01 are not visualized in the 2D-LD plot (Fig. 15B). All the MAF values for all
SNPs are provided in “show SNP data” of “help” (Fig. 15C).
A
B
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Updated: 2009/05/07