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Data description
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Data name
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Polymorphism Sequence
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DOI
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10.18908/lsdba.nbdc00114-001
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Description of data contents
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Information on polymorphisms (SNPs and insertions/deletions) and their flanking sequences
Derived from "Flat files" ftp://ftp.hgc.jp/pub/hgc/db/snp/imsSNP140508.fas and ftp://ftp.hgc.jp/pub/hgc/db/snp/imsIND140508.fas
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Data file
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File name :
jsnp_seq.zip
File URL :
File size :
10.6 MB
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Simple search URL
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http://togodb.biosciencedbc.jp/togodb/view/jsnp_seq#en
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Data acquisition method
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From "Screening Information"
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Data analysis method
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-
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Number of data entries
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197,195 entries
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Data detail
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Data item
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Description
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| Database Name |
database name
JSNP_SNP: single nucleotide polymorphism
JSNP_InsDel_IND: insertion/deletion
JSNP_InsDel_MIC: microsatelite |
| JSNP ID |
JSNP ID
ID starting with IMS-JST: from IMS and JST
ID starting with ssj: from RIKEN SNP Research Center or from Tokyo Women's Medical University |
| Allele Frequency |
(only in SimpleSearch pages) link to Allele Frequency of the same JSNP ID |
| Screening Information |
(only in SimpleSearch pages) link to Screening Information of the same JSNP ID |
| Mapping Information |
(only in SimpleSearch pages) link to Mapping Information of the same JSNP ID |
| Integrated List |
(only in SimpleSearch pages) link to Integrated List of the same JSNP ID |
| dbSNP ss# |
dbSNP ss (submitted SNP) number assigned |
| dbSNP rs# |
dbSNP rs (reference SNP) number assigned |
| 5' Flanking Sequence |
5' flanking sequence |
| Observed |
allele observed |
| 3' Flanking Sequence |
3' flanking sequence |
| Offset in Flanking Sequence |
position of the polymorphism in the flanking sequence |
| Total Length |
total length of the flanking sequence |
| Accession No. |
accession No. of the sequence for polymorphism screening |
| Offset in Record |
position of the polymorphism in the sequence for polymorphism screening |
| Comment Type |
1: the polymorphism overlaps with a repetitive sequence
2: the flanking sequence overlaps with a repetitive sequence |
| Gene Symbol |
gene where the polymorphism is found
(information from LocusLink, GenBank and Unigene) |
| JSNP previous ID |
JSNP previous ID
(IDs of IMS-JST104817 to IMS-JST105472 and IMS-JST075266 to IMS-JST075585 are reassigned with ssj IDs) |
| JSNP reference ID |
JSNP reference ID
(where multiple JSNP IDs are assigned to the same polymorphism) |
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