生信常用术语总结整理札记

可能是要入坑生信了么?不造唉,不过最近的工作基本围绕这些展开,来一波常用术语总结整理吧。

嗯,有错误的话,请评论下,告诉我,谢谢~

-->Amplicon Part  (扩增子Part)

--->1:Manifest (PDF only)   ( 清单(仅PDF))

中文解释:分析中使用的清单的名称。

英文解释:The name of the manifest used in the analysis.

--->2:Number of Amplicon Regions  (扩增子区域数)

中文解释:测序的扩增子区域数量。

英文解释:The number of amplicon regions that were sequenced.

--->3:Total Length of Amplicon Regions (扩增子区域的总长度)

中文解释:目标区域中测序碱基的总长度。

英文解释:The total length of the sequenced bases in the targeted region.


-->Read Level Part (Read 级别Part)

--->1:Total Aligned Reads (完全对齐的Reads)

中文解释:在与参考基因组对齐了的数据集中,通过过滤的reads总数。

英文解释:The total number of reads passing filter present in the data set that aligned to the reference genome.

--->2:Percent Aligned Reads (对齐Reads的百分比)

中文解释:通过与参考基因组对齐比对过滤的reads所占的百分比。

英文解释:The percentage of reads passing filter that aligned to the reference genome.


-->Base Level Part (碱基级别Part)

--->1:Percent Q30 (Q30的百分比)

中文解释:质量得分有30甚至更高的碱基所占的百分比。30是一个常用的标准

英文解释:The percentage of bases with a quality score of 30 or higher.

--->2:Total Aligned Bases(对齐了的碱基总数)

中文解释:在与参考基因组对齐了的数据集中的碱基总数。

英文解释:The total number of bases present in the data set that aligned to the reference genome.

--->3:Percent Aligned Bases (对齐了的碱基百分比)

中文解释:与参考基因组对齐了的碱基所占百分比。

英文解释:The percentage of bases that aligned to the reference genome.

--->4:Mismatch Rate (不匹配率)

中文解释:在所有循环匹配中,reads1和reads2均没有匹配到的平均百分比。

英文解释:The average percentage of mismatches across both reads 1 and 2 over all cycles.


-->Small Variants Part (小变异Part)

--->1:Total Passing (通过的总数量)

中文解释:通过变异质量过滤器的数据集中的变异总数量。

英文解释:The total number of variants present in the data set that passed the variant quality filters.

--->2:Percent Found in dbSNP (可以在dbSNP中发现的变异所占百分比)

中文解释:100*(dbSNP中的变异数量/变异数量)

英文解释:100*(Number of variants in dbSNP/Number of variants).

--->3:Het/Hom Ratio ( Het/Hom比率 )

中文解释:杂合变异的数目/纯合变异的数目

英文解释:Number of heterozygous variants/Number of homozygous variants.

--->4:Ts/Tv Ratio ( Ts/Tv比率 )

中文解释:通过质量过滤器的SNV的转换率/通过质量过滤器的SNV颠换率。转换是指嘌呤(A,G)或嘧啶(C,T)的交换。颠换是指嘌呤和嘧啶碱基之间的交换(例如:A到T)。

英文解释:Transition rate of SNVs that pass the quality filters divided by transversion rate of SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges between purine and pyrimidine bases (for example, A to T).


-->Variants by Sequence Context Part (序列上下文环境的变异Part)

--->1:Number in Genes (基因数目)

中文解释:属于基因的变异数量。

英文解释:The number of variants that fall into a gene.

--->2:Number in Exons (外显子数目)

中文解释:属于外显子的变异数量。

英文解释:The number of variants that fall into an exon.

--->3:Number in Coding Regions (编码区域的数目)

中文解释:属于编码区域的变异数量。

英文解释:The number of variants that fall into a coding region.

--->4:Number in UTR Regions (UTR区域的数目)

中文解释:属于非翻译区(UTR)的变异数量。

英文解释:The number of variants that fall into an untranslated region (UTR).

--->5:Number in Splice Site Regions (剪接位点区域的数目)

中文解释:属于剪接位点区域的变异数量。

英文解释:The number of variants that fall into a splice site region.


-->Variants by Consequence Part (结论变异Part)

--->1:Frameshifts (移码)

中文解释:引起移码的变异数量。

英文解释:The number of variants that cause a frameshift.

--->2:Non-synonymous (非同义)

中文解释:在编码区内,会引起氨基酸改变的变异数量。

英文解释:The number of variants that cause an amino acid change in a coding region.

--->3:Synonymous (同义)

中文解释:在编码区内,不会引起氨基酸改变的变异数量。

英文解释:The number of variants that are within a coding region, but do not cause an amino acid change.

--->4:Stop Gained (终止密码子获得)

中文解释:导致获得了额外终止密码子的变异数量。

英文解释:The number of variants that cause an additional stop codon.

--->5:Stop Lost (终止密码子丢失)

中文解释:引起终止密码子丢失的变异数量。

英文解释:The number of variants that cause the loss of a stop codon.


-->Variants Part (变异Part)

--->1:Chromosome (Chr)  (染色体)

中文解释:参考染色体的名称。

英文解释:Name of reference chromosome.

--->2:Position (Pos)  (定位)

中文解释:在参考染色体内的定位。

英文解释:Position within reference chromosome.

--->3:Reference Allele (Ref) (参考等位基因)

中文解释:参考等位基因。

英文解释:The reference allele.

--->4:Variant Allele (Alt) (变异等位基因)

中文解释:变异等位基因。

英文解释:The alt allele.

--->5:Variant Type (Type) (变异类型)

中文解释:变异的类型,包活单核苷酸变异(SNV)、插入、删除。

英文解释:Type of variant, including single nucleotide variant (SNV), insertion, and deletion.

--->6:Sequence Context (Context) (序列上下文环境)

中文解释:基于参考基因组的注释得出的变异位置。

英文解释:Location of the variant based on annotations of the reference genome.

--->7:dbSNP ID (dbSNP) (dbSNP ID)

中文解释:在单核苷酸多态性数据库(dbSNP)中的标识符,dbSNP是由国家生物技术信息中心(NCBI)开发和托管的不同物种内、跨域不同物种的遗传变异的免费公共存档。

英文解释:Identifier in the Single Nucleotide Polymorphism Database (dbSNP), a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI).

--->8:COSMIC ID (COSMIC) (COSMIC ID)

中文解释:癌症体细胞突变目录(CODMIC)数据库中变异的数字标识符。

英文解释:The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

--->9:ClinVar

中文解释:基于可自由访问的公共人类变异、表型之间关系的报告得出的临床意义。

英文解释:Clinical significance based on the freely accessible, public archive of reports of the relationships among human variations and phenotypes.

--->10:Variant Quality (Qual) (变异质量)

中文解释:活动规模的质量得分表明我们对这个单倍型的断言有多可靠。

英文解释:Phred-scaled quality score indicating how confident we are in this asserted haplotype.

--->11:Variant Frequency (Alt Freq) (变异频率)

中文解释:在所有被考虑的等位基因中,变异等位基因所占的比例。

英文解释:Proportion of the variant allele among all alleles being considered.

--->12:Total Depth (总深度)

中文解释:对齐到某个位置的reads数量。

英文解释:Number of reads aligned at this position.

--->13:Reference Allele Depth (Ref Depth) (参考等位基因深度)

中文解释:包含参考等位基因的reads数量。

英文解释:Number of reads containing the reference allele.

--->14:Variant Allele Depth (Alt Depth) (变异等位基因深度)

中文解释:包含变异等位基因的reads数量。

英文解释:Number of reads containing the variant allele.

--->15:Strand Bias (链偏差)

中文解释:偏差是一种序列化偏差。在这种偏差下,1个DNA链比其他DNA链更被偏向,这样可能会导致为一个等位基因对比另一个等位基因所观察到的证据量的不正确的评价。

英文解释:Strand bias is a type of sequencing bias in which 1 DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele versus the other.

--->16:Consequence (结果)

中文解释:如uswest.ensembl.org/info/genome/variation/predicted_data.html#consequences所描述的,被预测的转录后结果。

英文解释:Predicted transcript consequence as described at uswest.ensembl.org/info/genome/variation/predicted_data.html#consequences.


-->Coverage Part  (覆盖Part)

--->1:Amplicon Mean Coverage (扩增子的平均覆盖)

中文解释:与目标区域对齐的reads的总数/目标区域的数目。

英文解释:The total number of aligned reads to the targeted region divided by the number of targeted regions.

--->2:Uniformity of Coverage (Pct > 0.2*mean)  (覆盖平均度)

中文解释:目标基位置,即read深度大于平均区域目标覆盖深度的0.2倍的位置,所占的百分比。

英文解释:The percentage of targeted base positions in which the read depth is greater than 0.2 times the mean region target coverage depth.





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转载自blog.csdn.net/orange_612/article/details/79974609