Sample Mismatch Algorithm - Newport iServer MicroServer iTHX-M Operator's Manual

Sample Mismatch Algorithm

Mapping Tool Algorithms
Algorithms/formulas for the different mapping tools:
• Sample Mismatch Algorithm (see below)
• Filter Algorithms (see page 380)
The Sample Mismatch report uses the Mismatch score to determine if
two samples are the same. The Mismatch score for a single SNP is the
number of alleles shared between two individuals, either 0, 1, or 2. If
both individuals have the same genotype, two alleles are shared. The
table below lists the Mismatch scores for different genotype pairs.
Table E.1
Mismatch scores for SNP genotype calls
Genotype 1 Genotype 2
AA AA
AA AB
AA BB
AB AA
AB AB
AB BB
BB AA
BB AB
BB BB
Nocall Any call
The report uses the averaged Identity by State (IBS) metric, calculated
over a set of 30 to 50 common SNPs, as a measure of the number of
SNPs with shared alleles. The averaged IBS metric, or Mismatch score,
increases with the relatedness of the pair:
• Identical twins should have a Mismatch score of 1.95 - 2.0
Mismatch Score
2
1
0
1
2
1
0
1
2
Ignore
379