西亚试剂：：SNP命名规则

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)：

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#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

……

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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：

 

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