{"id":70253,"date":"2026-11-14T23:40:49","date_gmt":"2026-11-14T15:40:49","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70253"},"modified":"2026-11-14T23:40:49","modified_gmt":"2026-11-14T15:40:49","slug":"snpeff-two-transcripts-missense-intronic-codon","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/snpeff-two-transcripts-missense-intronic-codon\/","title":{"rendered":"SnpEff \u5b9e\u8dd1\uff5c\u540c\u4e00\u4e2a C\u2192A\uff0c\u4e3a\u4ec0\u4e48\u5728\u4e00\u4e2a\u8f6c\u5f55\u672c\u4e0a\u662f\u9519\u4e49\uff0c\u5728\u53e6\u4e00\u4e2a\u4e0a\u5374\u662f\u5185\u542b\u5b50\uff1f"},"content":{"rendered":"
\n

\u4e00\u4efd\u53d8\u5f02\u6ce8\u91ca\u8868\u91cc\uff0c\u540c\u4e00\u4e2a\u67d3\u8272\u4f53\u4f4d\u7f6e\u65e2\u5199\u7740\u9519\u4e49\u53d8\u5f02\uff0c\u53c8\u5199\u7740\u5185\u542b\u5b50\u53d8\u5f02\uff0c\u7a76\u7adf\u8be5\u5220\u53bb\u54ea\u4e00\u6761\uff1f\u5148\u770b\u8fd9\u4e24\u4e2a\u7ed3\u8bba\u5206\u522b\u5c5e\u4e8e\u54ea\u4e2a\u8f6c\u5f55\u672c\u3002\u6211\u4eec\u5b89\u88c5 SnpEff 5.2b\uff0c\u5efa\u7acb\u4e86\u4e00\u4e2a\u53ea\u6709\u4e00\u6761\u67d3\u8272\u4f53\u3001\u4e00\u4e2a\u57fa\u56e0\u548c\u4e24\u4e2a\u8f6c\u5f55\u672c\u7684\u5c0f\u578b\u6ce8\u91ca\u6570\u636e\u5e93\u3002\u4e24\u4e2a\u8f6c\u5f55\u672c\u5171\u4eab\u9996\u5c3e\u5916\u663e\u5b50\uff0c\u5176\u4e2d\u4e00\u4e2a\u591a\u542b\u4e00\u6bb5\u7f16\u7801\u5916\u663e\u5b50\u3002\u5728\u8fd9\u6bb5\u5e8f\u5217\u4e0a\u53ea\u6539\u4e00\u4e2a\u78b1\u57fa\uff0c\u4e24\u4e2a\u7ed3\u8bba\u679c\u7136\u540c\u65f6\u51fa\u73b0\u3002\u518d\u628a\u53d8\u5f02\u79fb\u52a8\u4e00\u4f4d\uff0c\u9519\u4e49\u53d8\u6210\u540c\u4e49\uff0c\u800c\u53e6\u4e00\u8f6c\u5f55\u672c\u4e0a\u7684\u5185\u542b\u5b50\u6ce8\u91ca\u4fdd\u6301\u4e0d\u53d8\u3002\u8fd9\u4e2a\u4f8b\u5b50\u53ef\u4ee5\u76f4\u63a5\u7528\u5bc6\u7801\u5b50\u8868\u9a8c\u7b97\u3002<\/p>\n

\u5148\u628a\u53c2\u8003\u5e8f\u5217\u4e0e\u8f6c\u5f55\u672c\u753b\u5728\u540c\u4e00\u5f20\u7eb8\u4e0a<\/h2>\n

\u4eba\u5de5\u67d3\u8272\u4f53\u957f\u4e00\u5343\u78b1\u57fa\uff0c\u4e24\u4e2a\u8f6c\u5f55\u672c\u90fd\u5728\u6b63\u94fe\u3002\u957f\u8f6c\u5f55\u672c\u5305\u542b\u4e09\u4e2a\u5916\u663e\u5b50\uff0c\u5750\u6807\u662f\u4e00\u767e\u96f6\u4e00\u81f3\u4e00\u767e\u4e09\u5341\u3001\u4e8c\u767e\u96f6\u4e00\u81f3\u4e8c\u767e\u4e09\u5341\u3001\u56db\u767e\u96f6\u4e00\u81f3\u56db\u767e\u4e8c\u5341\u4e00\u3002\u77ed\u8f6c\u5f55\u672c\u4fdd\u7559\u7b2c\u4e00\u6bb5\u548c\u6700\u540e\u4e00\u6bb5\uff0c\u4e2d\u95f4\u6574\u6bb5\u5728\u5b83\u7684\u6210\u719f\u8f6c\u5f55\u672c\u4e2d\u88ab\u8df3\u8fc7\u3002\u6211\u4eec\u8bbe\u7f6e\u4e86\u5b8c\u6574\u7684\u8d77\u59cb\u548c\u7ec8\u6b62\u5bc6\u7801\u5b50\uff0c\u6240\u6709\u7f16\u7801\u5757\u957f\u5ea6\u90fd\u662f\u4e09\u7684\u500d\u6570\uff0cGFF \u4e2d\u7684\u7f16\u7801\u76f8\u4f4d\u6309\u8fd9\u4e2a\u6a21\u578b\u8bbe\u5b9a\u3002\u8fd9\u8ba9\u6ce8\u91ca\u5dee\u5f02\u53ef\u4ee5\u5f52\u5230\u5916\u663e\u5b50\u9009\u62e9\uff0c\u800c\u4e0d\u81f3\u4e8e\u540c\u65f6\u6df7\u5165\u79fb\u7801\u3001\u65b9\u5411\u548c\u4e0d\u540c\u8d77\u59cb\u4f4d\u7f6e\u3002SnpEff \u5b98\u65b9\u81ea\u5efa\u6570\u636e\u5e93\u8bf4\u660e<\/a><\/p>\n

\u5bf9\u57fa\u56e0\u7ec4\u53d8\u5f02\u800c\u8a00\uff0c\u53c2\u8003\u78b1\u57fa\u548c\u66ff\u4ee3\u78b1\u57fa\u7531\u57fa\u56e0\u7ec4\u5750\u6807\u56fa\u5b9a\u3002\u8f6c\u5f55\u672c\u5750\u6807\u548c\u86cb\u767d\u7ed3\u679c\u9700\u8981\u6cbf\u5404\u8f6c\u5f55\u672c\u81ea\u5df1\u7684\u7f16\u7801\u8def\u5f84\u8ba1\u7b97\u3002\u540c\u4e00\u57fa\u56e0\u540d\u53ea\u662f\u544a\u8bc9\u8bfb\u8005\u8fd9\u4e9b\u8f6c\u5f55\u672c\u5c5e\u4e8e\u540c\u4e00\u57fa\u56e0\uff0c\u4e0d\u80fd\u4ee3\u66ff\u8f6c\u5f55\u672c\u7f16\u53f7\u3002\u7ed3\u6784\u4e0d\u540c\u7684\u4e24\u4e2a\u8f6c\u5f55\u672c\uff0c\u6709\u65f6\u7ed9\u51fa\u76f8\u540c\u7684\u86cb\u767d\u53d8\u5316\uff0c\u6709\u65f6\u4e00\u4e2a\u6839\u672c\u6ca1\u6709\u53ef\u8ba1\u7b97\u7684\u86cb\u767d\u53d8\u5316\u3002\u6574\u7406\u62a5\u8868\u65f6\u5e94\u4fdd\u7559\u57fa\u56e0\u7ec4\u53d8\u5f02\u952e\u3001\u8f6c\u5f55\u672c\u7f16\u53f7\u548c\u540e\u679c\u7c7b\u578b\u4e09\u5c42\u8eab\u4efd\uff0c\u518d\u51b3\u5b9a\u662f\u4ee5\u7b49\u4f4d\u3001\u8f6c\u5f55\u672c\u8fd8\u662f\u57fa\u56e0\u4e3a\u5355\u4f4d\u6c47\u603b\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u56db\u4e2a\u53d8\u5f02\u5404\u6709\u4e24\u6761\u6ce8\u91ca<\/h2>\n

\u6211\u4eec\u628a FASTA \u548c GFF3 \u4ea4\u7ed9 SnpEff \u65b0\u5efa\u6570\u636e\u5e93\uff0c\u518d\u901a\u8fc7\u5176\u6b63\u5f0f\u6ce8\u91ca\u5165\u53e3\u5904\u7406\u56db\u4e2a\u5355\u78b1\u57fa\u66ff\u6362\uff0c\u6700\u540e\u4ece VCF \u7684\u6ce8\u91ca\u5b57\u6bb5\u9010\u6761\u62c6\u51fa\u66ff\u4ee3\u7b49\u4f4d\u3001\u5f71\u54cd\u7c7b\u522b\u3001\u8f6c\u5f55\u672c\u3001\u5916\u663e\u5b50\u5e8f\u53f7\u4e0e\u86cb\u767d\u53d8\u5316\u3002\u9664\u4e86\u76ee\u6807\u4f4d\u70b9\uff0c\u8fd8\u9009\u4e86\u4e00\u5904\u5171\u4eab\u5916\u663e\u5b50\u7684\u540c\u4e49\u66ff\u6362\u548c\u4e00\u5904\u5171\u540c\u5185\u542b\u5b50\u7684\u5bf9\u7167\u3002\u6bcf\u4e2a\u53d8\u5f02\u660e\u786e\u653e\u5728\u53c2\u8003\u4e2d\u5b9e\u9645\u5b58\u5728\u7684\u78b1\u57fa\u4e0a\u3002\u8fd9\u4e2a\u6a21\u578b\u7528\u4e8e\u6838\u5bf9\u57fa\u56e0\u7ed3\u6784\u548c\u9605\u8bfb\u7ed3\u679c\uff0c\u6ca1\u6709\u7528\u5b83\u505a\u60a3\u8005\u98ce\u9669\u5224\u8bfb\u3002SnpEff \u8f93\u5165\u8f93\u51fa\u4e0e ANN \u5b57\u6bb5\u6587\u6863<\/a><\/p>\n

\n\n\n\n\n\n\n\n\n
\u4f4d\u7f6e\u4e0e\u53d8\u5316<\/th>\ntxA\uff0c\u4e09\u4e2a\u5916\u663e\u5b50<\/th>\ntxB\uff0c\u8df3\u8fc7\u4e2d\u95f4\u5916\u663e\u5b50<\/th>\n<\/tr>\n<\/thead>\n
112\uff0cT\u2192A<\/td>\n\u540c\u4e49\uff0cp.Ala4Ala<\/td>\n\u540c\u4e49\uff0cp.Ala4Ala<\/td>\n<\/tr>\n
214\uff0cC\u2192A<\/td>\n\u9519\u4e49\uff0cc.44C>A\uff0cp.Ala15Asp<\/td>\n\u5185\u542b\u5b50\uff0cc.30+84C>A<\/td>\n<\/tr>\n
215\uff0cT\u2192C<\/td>\n\u540c\u4e49\uff0cc.45T>C\uff0cp.Ala15Ala<\/td>\n\u5185\u542b\u5b50\uff0cc.30+85T>C<\/td>\n<\/tr>\n
302\uff0cT\u2192A<\/td>\n\u5185\u542b\u5b50\uff0cc.60+72T>A<\/td>\n\u5185\u542b\u5b50\uff0cc.31-99T>A<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u540c\u4e00\u53d8\u5f02\u6709\u4e24\u79cd\u540e\u679c\u3002\u81ea\u5efa\u4e00\u4e2a\u542b\u4e24\u6761\u8f6c\u5f55\u672c\u7684\u6570\u636e\u5e93\uff0c\u4ece\u5bc6\u7801\u5b50\u590d\u6838
\u81ea\u5efa\u4e00\u4e2a\u542b\u4e24\u6761\u8f6c\u5f55\u672c\u7684\u6570\u636e\u5e93\uff0c\u4ece\u5bc6\u7801\u5b50\u590d\u6838 ANN \u5b57\u6bb5\u3002<\/figcaption><\/figure>\n

\u7b2c\u4e8c\u767e\u4e00\u5341\u56db\u4f4d\u5728\u957f\u8f6c\u5f55\u672c\u4e0a\u5904\u4e8e\u7b2c\u4e8c\u4e2a\u5916\u663e\u5b50\u3002\u7b2c\u4e00\u6bb5\u7f16\u7801\u4e09\u5341\u4e2a\u78b1\u57fa\uff0c\u518d\u4ece\u7b2c\u4e8c\u6bb5\u8d77\u70b9\u4e8c\u767e\u96f6\u4e00\u8ba1\u5165\u5341\u56db\u4e2a\uff0c\u5f97\u5230\u7f16\u7801\u5750\u6807\u56db\u5341\u56db\u3002\u5b83\u4f4d\u4e8e\u7b2c\u5341\u4e94\u4e2a\u5bc6\u7801\u5b50\u7684\u7b2c\u4e8c\u4e2a\u4f4d\u7f6e\u3002\u53c2\u8003\u5bc6\u7801\u5b50\u4e3a GCT\uff0c\u4ee3\u8868\u4e19\u6c28\u9178\uff0c\u628a\u4e2d\u95f4 C \u6539\u4e3a A \u5f97\u5230 GAT\uff0c\u7f16\u7801\u5929\u51ac\u6c28\u9178\u3002\u518d\u770b\u7d27\u90bb\u7684\u4e8c\u767e\u4e00\u5341\u4e94\u4f4d\uff0c\u6539\u53d8\u7684\u662f\u8be5\u5bc6\u7801\u5b50\u7684\u7b2c\u4e09\u4e2a\u78b1\u57fa\uff0cGCT \u53d8\u6210 GCC\uff0c\u4ecd\u7f16\u7801\u4e19\u6c28\u9178\u3002\u8f6f\u4ef6\u7ed9\u51fa\u7684\u4e00\u4e2a\u9519\u4e49\u3001\u4e00\u4e2a\u540c\u4e49\uff0c\u53ef\u4ee5\u4e0e\u9010\u5b57\u7ffb\u8bd1\u4e00\u4e00\u5bf9\u7167\u3002<\/p>\n

\u77ed\u8f6c\u5f55\u672c\u5728\u4e00\u767e\u4e09\u5341\u4e4b\u540e\u76f4\u63a5\u63a5\u5230\u56db\u767e\u96f6\u4e00\uff0c\u56e0\u6b64\u4e8c\u767e\u4e00\u5341\u56db\u4e0e\u4e8c\u767e\u4e00\u5341\u4e94\u5bf9\u5b83\u90fd\u4f4d\u4e8e\u5185\u542b\u5b50\u3002\u76f8\u5bf9\u4e8e\u4e0a\u4e00\u7f16\u7801\u5916\u663e\u5b50\u672b\u7aef\uff0c\u4e24\u8005\u5206\u522b\u6807\u4e3a\u52a0\u516b\u5341\u56db\u548c\u52a0\u516b\u5341\u4e94\uff0c\u86cb\u767d\u53d8\u5316\u680f\u4e3a\u7a7a\u3002\u8fd9\u91cc\u7684\u7a7a\u503c\u6709\u660e\u786e\u7684\u7ed3\u6784\u542b\u4e49\uff0c\u4e0d\u5e94\u5728\u6570\u636e\u6e05\u6d17\u65f6\u586b\u6210\u201c\u86cb\u767d\u672a\u6539\u53d8\u201d\u3002\u518d\u770b\u7b2c\u4e09\u767e\u96f6\u4e8c\u4f4d\uff0c\u4e24\u6761\u8f6c\u5f55\u672c\u90fd\u7ed9\u51fa\u5185\u542b\u5b50\u540e\u679c\uff0c\u4f46\u7f16\u7801\u5750\u6807\u4e00\u6761\u4ece\u4e0a\u4e2a\u8fb9\u754c\u5f80\u540e\u52a0\u4e03\u5341\u4e8c\uff0c\u53e6\u4e00\u6761\u4ece\u4e0b\u4e2a\u8fb9\u754c\u5f80\u524d\u51cf\u4e5d\u5341\u4e5d\u3002\u5750\u6807\u8868\u8fbe\u4e0d\u540c\u4e0d\u7b49\u4e8e\u57fa\u56e0\u7ec4\u4f4d\u7f6e\u4e0d\u4e00\u81f4\u3002<\/p>\n

java -Xmx512m -jar snpEff.jar build -gff3 -noCheckCds -noCheckProtein -c snpEff.config toy\r\njava -Xmx512m -jar snpEff.jar ann -noStats -c snpEff.config toy input.vcf > annotated.vcf\r\nbcftools query -f '%CHROM\\t%POS\\t%REF\\t%ALT\\t%INFO\/ANN\\n' annotated.vcf\r\n<\/code><\/pre>\n
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