[Genome] humanStrand and chimpStrand in the table snp126orthoPanTro2RheMac2 seem to be mixed up.

[Sang Chul Choi]

Hi,

Firstly, thank you for the wonderful job of the UCSC genome browser
especially for the table, snp126orthoPanTro2RheMac2. I want to be
clear about the fields of the table focusing on "strand."

The table information is as follows that I want to ask a question about:
genome: Human
assembly: Mar. 2006
group: Variation and Repeats
track: SNPs
table: snp126orthoPanTro2RheMac2

I want to know the following things and the table is very helpful.
1. What are two alleles for a SNP?
2. What is the DNA type of the SNP in human genome?
3. What is the DNA type of the SNP in chimp genome?

For the question number 1, the field name, "humanObserved", should
give the answer. For the other two questions of 2 and 3,
"humanAllele", "humanStrand", "chimpAllele", and "chimpStrand" might
hint the answers. When both human and chimp strands are '+', the
answers of the question 2 and 3 are clear.

i.e.
name humanObserved humanAllele humanStrand chimpAllele chimpStrand
rs3056 A/G     A       +       A       +

But, if either strand is '-' or negative, then I am so clear what are
the answers of the question 2 and 3.

i.e.
rs3177  C/T     A       -       T       -

humanAllele is A, and its complementary DNA type (T) is the human
allele in the genome. chimpAllele is T, but the complementary is "A"
which is not either of SNP alleles (C/T). I looked for this rs3177 in
the UCSC genome browser and this is the summary of the SNP:
============================================
Summary: T>C/T (chimp allele displayed first, then '>', then human alleles)
Strand: -
Observed: C/T
Reference allele: T
Chimp Allele: T
Macaque Allele: T
============================================
According to this information, human allele (Reference allele) is T,
which makes sense because humanStrand is '-' and the complementary of
A is T. The chimpAllele is still 'T' rather than 'A' that I expected
before.
I checked two more examples whose human and chimp strand are different.
Here is my conclusion and I want to be sure if this is correct.
If humanStrand is '-' or negative, then we should complementarize the
humanAllele. The chimpStrand does not matter, though. The chimp allele
is just chimpAllele whether chimpStrand is positive or negative.

rs14068 A/G     A       +       G       -
============================================
Summary: G>A/G (chimp allele displayed first, then '>', then human alleles)
Strand: +
Observed: A/G
Reference allele: A
Chimp Allele: G
Macaque Allele: G
============================================

rs15928 A/T     T       -       T       +
============================================
Summary: T>A/T (chimp allele displayed first, then '>', then human alleles)
Strand: -
Observed: A/T
Reference allele: A
Chimp Allele: T
Macaque Allele: T
============================================

Thank you,

Sang Chul


-- 
===============================
Live, Learn, and Love!
E-mail : goshng shopt gmail dot com
===============================