一般写法是这样: dbSNP后面跟featureID. featureID一般是rs/ss后跟7-8位数字, 比如: rs12345678或者dbSNP|rs12345678 以下是老鼠(Mus muculas)的1号染色体上SNP列表格式(部分): ------------------------------------------------------------------------ #taxid chromosome chrStart chrEnd orientation contig cnt_start cnt_stop cnt_orient featureName featureId featureType groupLabel weight 10090 1 3007431 3007431 + NT_039169.2 7431 7431 + rs6357429 dbSNP:6357429 SNP C57BL/6J 3 10090 1 3063273 3063273 + NT_039169.2 63273 63273 + rs6351828 dbSNP:6351828 SNP C57BL/6J 3 10090 1 3063445 3063445 + NT_039169.2 63445 63445 + rs6365082 dbSNP:6365082 SNP C57BL/6J 3 10090 1 3064055 3064055 + NT_039169.2 64055 64055 + rs6368438 dbSNP:6368438 SNP C57BL/6J 3 …… -------------------------------------------------------------------------- 说明:第一个SNP的位置是3007431 - 3007431(也就是只有一个位点)。featureName是rs6357429,featureID是6357429,写作dbSNP:6357429. 以下是dbSNP数据库的rs_fasta格式:(以上例中rs6357429为例): >gnl|dbSNP|rs6357429_allelePos=251totallen=501|taxid=10090|snpClass=1|alleles='A/G'|mol=genomic|build=116 GACAGTCCCC ATCTTTCCAT CATTCTTCTC AGTTTATTCA TACATGTTTT AATTTCCATA GTTTTATTAT GTTCCTTTGG GCTTTTTTTC TGCCCCCCCC CCTTTTTGTG CCTTGTGATT CTTTTTAAGA CTTGTTTATT TGAGAATAGA TAAGCAGGGA CTACTTGTGA GCAAAGGCTT TCCCAAGTCA AGCCTACTGG AGGTTCTAGG ATCCATCACT CTAGCCTTTC CTGAGGATTA GGCTTTTCCC R GAGTTGAGTG TAACTTTTTC CATCAGTTTT AATACATTAA GCAGCTTATC TCTGCTTCAT TTTAGAAACC TGTAATCTGT TGCTTTGCCT GCTGTCTGCC CGAGGAACTA CAATTCTAAC ATGCTGTGTT CCTAGTGTAT ATTCTCAGCG GCTTCCAGAC AAAGCTGCTT GTTCCATCAG CAGTGCATCC AGTACCTGTT GGTGGTCTAT TAGTAGTCCA CATCAGGTGA GACAGATGGA GTCCTTCTGG 说明: gnl: object-type=general dbSNP: Database name rs6357429: dbSNP rs# or ss# allelePos=251: Offset of SNP in sequence totallen=501: Total length of sequence taxid=10090: taxID snpClass=1: 1:insertion/deletion 2:microsatellite 4:unclassified heterozygous 3:named without allele sequence 5:or no variation 6:. alleles='A/G': List of alleles rs_fasta格式详细说明请看: ftp://ftp.ncbi.nih.gov/snp/00readme.txt |
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