Snp Position Problem
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2
Entering edit mode
10.2 years ago
Biomed 4.7k

I need help regarding snp positions on dbsnp130. I downloaded the data files for dbsnp130 from UCSC download area dbsnp 130 txt and dumped it into a mysql database. When I query this database I can successfully get records for snps but when I try to look at the UCSC genome browser the data doesn't match. I use hg18 for the genome browser so it is not the mismatch between dbsnp130's coordiate system and the browsers but I can't understand what the problem is. Here is an example: in the dbsnp130 mysql table there is an entry for

    mysql> select * from snp130 where chrom="chr10" and chromStart>"99499150" and chromEnd<"99499550";
+------+-------+------------+----------+------------+-------+--------+---------+---------+----------+---------+-----------+------------------------------------------------------------------+----------+---------+--------+---------+--------+
| bin  | chrom | chromStart | chromEnd | name       | score | strand | refNCBI | refUCSC | observed | molType | class     | valid                                                            | avHet    | avHetSE | func   | locType | weight |
+------+-------+------------+----------+------------+-------+--------+---------+---------+----------+---------+-----------+------------------------------------------------------------------+----------+---------+--------+---------+--------+
| 1344 | chr10 |   99499330 | 99499331 | rs35817116 |     0 | +      | A       | A       | A/C      | genomic | single    | unknown                                                          |        0 |       0 | intron | exact   |      1 | 
| 1344 | chr10 |   99499357 | 99499357 | rs35737710 |     0 | +      | -       | -       | -/C      | genomic | insertion | unknown                                                          |        0 |       0 | intron | between |      1 | 
| 1344 | chr10 |   99499362 | 99499363 | rs10748707 |     0 | +      | A       | A       | A/G      | genomic | single    | by-cluster,by-frequency,by-2hit-2allele,by-hapmap,by-1000genomes | 0.482787 | 0.09116 | intron | exact   |      1 | 
+------+-------+------------+----------+------------+-------+--------+---------+---------+----------+---------+-----------+------------------------------------------------------------------+----------+---------+--------+---------+--------+
3 rows in set (0.00 sec)

But when I go to the genome browser to view this region and enable the dbsnp130 I can not see these snps. Any ideas why? Thanks

dbsnp position snp genome ucsc • 2.3k views
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7
Entering edit mode
10.2 years ago
Mitch Skinner ▴ 660

The version you have loaded into your database is the hg19 one:

$ gzip -cd hg18/database/snp130.txt.gz | grep rs35817116
1344    chr10   99489320    99489321    rs35817116  0   +   AA  A/C genomic single  unknown 0   0   intron  exact   1
$ gzip -cd hg19/database/snp130.txt.gz | grep rs35817116
1344    chr10   99499330    99499331    rs35817116  0   +   AA  A/C genomic single  unknown 0   0   intron  exact   1
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Thanks a lot, I hate it when I make such an obvious mistake. New resolution: Stop working after 2 am :)

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