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Related documents:
Minimal SNP (shown in red italics) needed to unambiguously distinguish haplotypes seen more than once within haplotype blocks chosen to give the lowest ratio of observed to expected haplotype heterozygosity, by population group
Please note that this an experimental resource which is still under test.Please email Ross Lazarus if you have comments or find any errors or anomalies
Group=Cases
[1, 4]
[1, 2, 3]
TTT (327, 31.9%)
TCA (281, 59.4%)
TCT (200, 78.9%)
CCA (169, 95.4%)
CCT (31, 98.4%)
TTA (16, 100.0%)
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Group=Controls
[1, 4]
[1, 2, 3]
TTT (292, 28.3%)
TCA (258, 53.3%)
TCT (202, 72.9%)
CCA (180, 90.3%)
TTA (76, 97.7%)
CCT (24, 100.0%)
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| Haplotype counts inferred by Phase*. |
| Gene = CD209, Minimum allele freq. in ANY population= 0.100, 3 SNP, 1028 Subjects
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| Note that the haplotypes shown below comprise alleles at |
| the following SNP locations in the order show. The first column |
| is the allele position in the haplotype. The SNP column is the |
| SNP position in the reference sequence (1=first base). The RelativeOffset column |
| is the SNP offset relative to the Gene transcription start codon. |
| # | SNP | RelativeOffset |
| 1 | 4674 | -336 |
| 2 | 4871 | -139 |
| 3 | 11456 | 6446 |
*
The PHASE software package was used to generate the contents of this output file.
Custom written Python scripts (available on request) were used to create the input files for
PHASE (from the raw data files in SeattleSNPs "prettybase" format available
elsewhere on this site) and also to process the PHASE output into more useful formats.
PHASE uses MCMC methods and is available from http://www.stats.ox.ac.uk/mathgen/software.html .
The results were obtained by running PHASE independently for each of the separate
groups shown and amalgamating the results.
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