Data used in Figure SM-6 in Supplementary Methods of
Sjoerd Repping,..., Steve Rozen.
"High mutation rates have driven extensive structural polymorphism among human Y chromosomes."
Nature Genetics, 38(4):463-467 (2006)
This file contains:
- A numbered list of SNP identifiers used within our lab.
- A matrix of SNP alleles. The two lines at the top of the matrix are the number of the SNP identifier. For example, the 31st column is labeled with 3 in the first row and 1 in the second row, referring to SNP 31 in the list above, which is NLGN4Y+135. These numbers are specific to this file, and do not in general correspond to the dbSNP PAGE|S99999 numbers.
Each row in the matrix gives the alleles of one sample. So by scrolling down column 31, one can see that the sample from haplogroup E3b3 had the rare (in this case, derived) allele at NLGN4Y+135.
One can translate back from haplogroup designations
by referring to Supplementary Table 1.
This file lets one find the STS info for a particular SNP, and
lets one translate from the SNP identifier used
within our lab to the dbSNP PAGE|S99999 identifier.
This file provides multiple tab-separated columns:
| Column |
Contents |
| 1 |
dbSNP SNP id (format PAGE|S99999) |
| 2
|
SNP identifier used within our lab (item 1 in file repping-et-al-2006-fig-SM-6-matrix.txt) |
| 3 |
the gene or pseudogene in which the SNP was found |
| 4 |
a nearby exon. |
| 5 | one of the SNP alleles |
| 6 | the other SNP allele |
| 7 |
the following info from dbSTS, separated by "bars": accession|unknown identifer|STS "name"|primer A sequence|primer B sequence
|
|
8
|
the STS sequence to the left of the SNP
|
|
8
|
the STS sequence to the right of the SNP
|
Steve Rozen
Last updated Sept 27, 2006