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
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written
by
Biomed
1 answer
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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written
by
Mitch Skinner
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