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Data description
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Data name
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Mapping Information
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DOI
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10.18908/lsdba.nbdc00114-004
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Description of data contents
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Information from mapping polymorphisms on the genome.
Derived from "Dump JSNP" http://snp.ims.u-tokyo.ac.jp/map/cgi-bin/Dump/snp_region_filter.cgi .
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Data file
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File name :
jsnp_dump.zip
File URL :
File size :
24 MB
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Simple search URL
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http://togodb.biosciencedbc.jp/togodb/view/jsnp_dump#en
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Data acquisition method
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From "Screening Information" and "Allele Frequency"
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Data analysis method
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The location of the SNPs are mapped to the RefSeq （GRCh37） contig sequence, masked by MaskerAid, using BLAST with the SNP flanking sequence, after e-PCR preformed with the primers for amplification to extract their screened regions.
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Number of data entries
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980,939 entries
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Data detail
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Data item
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Description
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| snp_id |
ID of JSNP |
| snp_type |
snp type: SNP or IND (insertion/deletion) |
| 5_flank_seq |
5'-flanking sequence of the snp |
| na_var |
nucleic acids variation |
| 3_flank_seq |
3'-flanking sequence of the snp |
| for_primer |
forward primer sequence for e-PCR |
| back_primer |
backward primer sequence |
| product_size |
PCR product size |
| freq_minor |
minor allele frequency of the snp (-1: no frequency information) from JSNP |
| freq_major |
major allele frequency of the snp from JSNP |
| chr |
chromosome number that the snp is mapped |
| chr_start |
start position of the snp in the chromosome |
| chr_end |
end position of the snp in the chromosome |
| chr_direct |
direction of the flanking sequences against the chromosome |
| contig_acc |
ACC of genomic contig (RefSeq NT) that the snp is mapped |
| contig_start |
start position of the snp in the genomic contig |
| contig_end |
end position of the snp in the genomic contig |
| contig_direct |
direction of the flanking sequences against the genomic contig |
| hit_count |
number of hit (mapped positions of the snp against genome) |
| gene_na_acc |
ACC of a gene (RefSeq NM/XM) that the snp is mapped |
| gene_aa_acc |
ACC of the gene (RefSeq NP/XP) that the snp is mapped |
| symbol |
symbol of gene that the snp is mapped |
| locus_id |
ID of gene (LocusLink) that the snp is mapped |
| gene_direct |
direction of the flanking sequences against the direction of the gene:
if the directions of the flanking sequences and of the gene are the same, this is "+"; otherwise "-". |
| str_type |
gene structure that the snp is mapped: CDS, exon, intron, 5'-UTR, 3'-UTR |
| aa_var |
amino acids variation |
| codon_var |
codon variation |
| codon_posi |
snp postion in the codon |
| dbsnp_rs_id |
dbSNP rs (reference SNP) number assigned |
| dbsnp_ss_id |
dbSNP ss (submitted SNP) number assigned |
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