Panel size

Number of linked markers

Number of linked SNPs

Number of linked STRs

Linkage

Bias


x

0

0

0

Unlinked

Both

x

2

2

0

OnePairLinked

SNP

x

2

0

2

OnePairLinked

STR

x

0.125x

0.125x

0

HalfQuarterLinked

SNP

x

0.125x

0

0.125x

HalfQuarterLinked

STR

x

0.125x

0.0625x

0.0625x

HalfQuarterLinked

Both

x

0.25x

0.25x

0

QuarterLinked

SNP

x

0.25x

0

0.25x

QuarterLinked

STR

x

0.25x

0.125x

0.125x

QuarterLinked

Both

x

0.5x

0.5x

0

HalfLinked

SNP

x

0.5x

0

0.5x

HalfLinked

STR

x

0.5x

0.25x

0.25x

HalfLinked

Both

x

0.75x

0.5x

0.25x

ThreeQuarterLinked

SNP

x

0.75x

0.25x

0.5x

ThreeQuarterLinked

STR

x

0.75x

0.375x

0.375x

ThreeQuarterLinked

Both

x

x2

0.5x

0.5x2

AlmostLinked

SNP

x

x2

0.5x2

0.5x

AlmostLinked

STR

x

x

0.5x

0.5x

FullyLinked

Both

 The “PanelSize” is the number of markers in each panel and in each panel, half markers are SNPs and the other half markers are STRs. In this table to illustrate the rules of design, “PanelSize” is set to “x”
 The variable “Linkage” is defined as the percentage of linked markers among the total. For example, if the “PanelSize” is x, the number of linked markers is 0.5x, then the “Linkage” equals to “HalfLinked”. The “OnePairLinked” and “AlmostLinked” have unfixed percentage of linked markers but hold the numbers of linked or unlined markers. If there are only 2 linked markers, the “Linkage” is defined as “OnePairLinked”; if there are only 2 unlinked markers and all others are linked, the “Linkage” is defined as “AlmostLinked”
 The variable “Bias” is defined as the distribution of linked markers. If the number of linked SNPs is larger than linked of STRs, the “Bias” equals to “SNP”; in contrast, if the number of linked SNPs is smaller than linked STRs, the “Bias” equals to “STR”; but if the number of linked SNPs and STRs are the same, “Bias = Both”. When the linked markers are less than 50% of total markers, in the biased groups, all linked markers are the same type of markers the biased one. When the linkage is higher than “HalfLinked”, all the biased markers are linked, and the unlinked markers are found on the other type