Newport iServer MicroServer iTHX-M, Operator'S Manual

Page: 217 / 414

Chapter 6 | Working with Mapping Data
209
two individuals or samples. The averaged IBS metric, or Mismatch
score, increases with the relatedness of the pair:
• Identical twins and samples from the same person should have
Mismatch scores ranging from 1.95 to 2.0.
• Sib pairs and parent-offspring should have Mismatch scores
ranging from 1.3 to1.8
• Unrelated pairs should have Mismatch scores from 0.9 to 1.3.
The Sample Mismatch report can be run in two modes:
• If no sample attributes are specified, all sample matches are
reported.
The report shows every chip pair with significant SNP overlap.
For more information, see Checking for Sample Matches, on page 210 .
• If sample attributes are specified, the sample mismatches are also
reported.
The report can flag the following types of problems:
- .chp files with the same sample IDs but a different common
SNP pattern or gender.
- .chp files with different sample IDs but the same common
SNP pattern.
For more information, see Checking for Sample Mismatches, on
page 219 .
For more information about the calculation of the Mismatch score, see
Sample Mismatch Algorithm, on page 379 .
To open the Sample Mismatch Report dialog box:
1.
Click the Sample Mismatch Report button in the
Genotyping Views shortcut bar; or
Select Tools Sample Mismatch Report... from the menu bar.
The Sample Mismatch report dialog box appears (Figure 6.26) .
GTYPE_manual.book Page 209 Wednesday, August 2, 2006 11:31 AM