Dear Rhead,
For the first example, what record should I keep?
when I look the rsID 3115865 in dbSNP
page(http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3115865), I cannot
find the chromosome position in the dbSNP page. Why you assign 741579 on chr1
for this rsID? While for the second rsID, I found the right chr position for it.
Did you have a detailed illustration on the UCSC FAQ website showing why you
keep two(sometimes three or more) rsID for the identical chr position?
For example, for the three records for one chr position, which should I keep,
the first or the last one, or none of them is a confident SNP???
585 chr1 12479 12480 rs62028715 0 + C C
C/G genomic single unknown 0 0 unknown exact 3
MultipleAlignments BCMHGSC_JDW, 0
585 chr1 12479 12480 rs78725323 0 - C C
C/G genomic single unknown 0 0 unknown exact 3
MultipleAlignments ENSEMBL, 1 C, 2.000000,
1.000000, maf-5-some-pop,maf-5-all-pops
585 chr1 12479 12480 rs78735090 0 + C C
C/G genomic single by-frequency 0.48 0.09798 unknown exact 3
MultipleAlignments 1 ENSEMBL, 2 G,C,
4.000000,6.000000, 0.400000,0.600000, maf-5-some-pop,maf-5-all-pops
But for the SNP on the following chr position:
585 chr1 10439 10440 rs112155239 0 + C C
A/C genomic single unknown 0 0 unknown exact 1
1 BCM-HGSC-SUB, 0
585 chr1 10439 10440 rs112766696 0 + C C
-/C genomic deletion unknown 0 0 unknown exact 1
1 BUSHMAN, 2 -,C, 1.000000,1.000000,
0.500000,0.500000,
which record should I regard as confident? for they both have no
"MultipleAlignments" annotation.
I am eagerly to know all the details and which record(or rsID) should I
consider as confident.
All my best,
Jiangtao
BGI-Shenzhen
On May 28, 2011, at 9:01 AM, Brooke Rhead wrote:
> Hi Jiangtao,
>
> The engineer who works on SNPs here took a quick look at your examples. For
> the first one, there may have been a strand error that caused dbSNP to fail
> to cluster the newer SNP (rs61770168) together with the older SNP
> (rs3115865). For the second example, you may just want to ignore rs28658281,
> since it aligns to multiple places in the genome and has been given a higher
> weight by dbSNP.
>
> In both cases, you should check out dbSNP's pages (which are linked on the
> details pages in the Genome Browser). For instance:
> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3115865
>
> There you can see the full report on each reference SNP (which start with an
> "rs" -- we only show reference SNPs in the Genome Browser), and you can look
> at the list of submitter SNPs (which start with "ss") that were used to
> determine each reference SNP.
>
> You might also want to report these cases directly to dbSNP at
> [email protected].
>
> I hope this is helpful. If you have further questions for UCSC, please feel
> free to contact us again at [email protected].
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
>
> On 05/26/11 21:58, Tao Jiang wrote:
>> Dear UCSC bioinformatic scientists:
>> When use the file "snp132.txt.gz" downloaded from UCSC, I found a confusion
>> question: Why the SNPs that have exactly the same start and end coordinates
>> have different rsID, and sometimes have different allele frequency? Which
>> record is the refSNP record from NCBI dbSNP 132?
>> The following are two examples:
>> 1. 590 chr1 741578 741579 rs3115865 0 - T T
>> A/G genomic single by-cluster,by-hapmap 0 0
>> unknown exact 3 590 chr1 741578 741579 rs61770168 0
>> + T T C/T genomic single unknown 0 0
>> unknown exact 1 1 2. 707 chr22 16050993
>> 16050994 rs7288968 0 + G G C/G
>> genomic single by-cluster,by-2hit-2allele,by-hapmap 0 0
>> unknown exact 1 2 BCM_SSAHASNP,CSHL-HAPMAP, 0
>>
>> 707 chr22 16050993 16050994 rs28658281 0 -
>> G G C/G genomic single by-cluster,by-frequency 0.375
>> 0.216506 unknownexact 3 MultipleAlignments 6
>> BCM-HGSC-SUB,BCMHGSC_JDW,BGI,ENSEMBL,HGSV,SSAHASNP, 2 G,C,
>> 6.000000,2.000000, 0.750000,0.250000, maf-5-some-pop,maf-5-all-pops
>> I am looking forward to hearing from you as soon as possible. Thanks a lot!
>> All my best,
>> Jiangtao
>> BGI-Shenzhen
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
