A successful download from hgTables of table 'snp129'
gives 15,625,346 data rows + 1 header row x 18 columns.
My question concerns odd values in column 2 'chrom'.
A total of 117,375 rows in the table show chromosome
names of the form 'chr00_random'. These are rows
15,321,501 through 15,438,875. A total of 186,471
further rows show names 'chr5_h2_hap1', chr22_h2_hap1',
'chr6_cox_hap1' or 'chr6_qbl_hap2'. These are rows
15,438,876 through 15,625,346. Please, how should I
interpret these values for column 2 'chrom' ?
The button for [describe table schema] in the table
browser is informative about the values in other fields,
but not these in 'chrom'. I have downloaded and searched
the 'b129_..._36_3.bcp.gz' files directly from dbSNP and
I cannot find any such chromosome names. Where do these
values come from ?
- many thanks -
Tom Blackwell
University of Michigan, Biostatistics
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
