教育教学   Education
联系我们   Contact
搜索   Search
你的位置:首页 > 教育教学 > 科研软件

“mixing ratio and patterns”使用说明

2019/12/4 9:58:09      点击:

“mixing ratio and patterns”使用说明

邓楚薇,陈鹏,陈峰

“mixing ratio and patterns”是一个用于预测DNA混合样本的混合比例及混合模式的软件。可以通过各等位基因的测序深度,推算两人或三人DNA混合样本的混合比例及混合模式,使用者可以根据这些信息,将等位基因分配给各贡献者,获得贡献者各自的基因型。

表格“mixing ratio of 2 contributors”用于计算两人混合物的混合比例和混合模式,表格“mixing ratio of 3 contributors”用于计算三人混合物的混合比例和混合模式。

在表格“mixing ratio of 2 contributors”中,单元格A2及A3用于输入只出现两个等位基因的位点的等位基因测序深度。单元格D2:D5显示的是两人混合物中出现两个等位基因的位点可能的混合模式,单元格E2:E5显示输入的等位基因测序深度可能是哪种混合模式和混合比例,当测序深度不能被相应的混合模式解释的时候,显示为FALSE;当测序深度能够被解释的时候则显示为相应的混合比例。单元格A8:C8用于输入只出现三个等位基因的位点的等位基因测序深度,D8:E10显示可解释等位基因测序深度的混合模式和混合比例。

在表格“mixing ratio of 3 contributors”中,单元格A3:C3、A35:D35及A60:E60分别用于输入出现三个、四个和五个等位基因的位点的等位基因测序深度,单元格A6:B31、A38:B56及A63:B68分别显示可解释相应等位基因测序深度的混合模式和比例。

注意事项:

1.各位点输入的等位基因测序深度之和需为1000,若不为1000,需等比例放大或缩小至和为1000再填入。

2.输入时从左到右依次将等位基因测序深度从小到大输入。

3.默认两人混合时,各混合模式下混合比例为1:X(1<X);三人混合时,各混合模式下混合比例为1:X:Y(1<X<Y)。

4.混合模式的命名规则如下:(1)命名分为两个部分,字母部分代表各贡献者是纯合子(HO)还是杂合子(HE);(2)字母部分按照贡献者的贡献比例从小到大依次排列;(3)数字部分代表各贡献者之间共享等位基因的情况,在两人混合物中数字部分为一位,表示两个贡献者之间共享等位基因的数量;三人混合物中数字部分有四位,第一个数字代表三位贡献者都拥有的等位基因的数量,第二位数字代表第一位贡献者和第二位贡献者共享等位基因的数量,第三位代表第一位贡献者和第三位贡献者共享等位基因的数量,第四位代表第二位贡献者和第三位贡献者共享等位基因的数量。

Mixing ratio and patterns

Chuwei Deng, Peng Chen and Feng Chen

“Mixing ratio and patterns”is a convenient tool forinterpreting genotypes of DNA mixturesof two or three contributors. By using this tool properly,mixing pattern and mixing ratio of DNA mixtures can be inferred based on the sequencing depth of alleles. You can use the results of this tool and then assign alleles to each contributor. Here is the tutorial for “mixing ratio and patterns”.

Table “mixing ratio of 2 contributors” is for DNA mixtures of two individuals. Table “mixing ratio of 3 contributors” is for DNA mixtures of three individuals.

In table “mixing ratio of 2 contributors”, if the detected locus has only two alleles, the sequencing depth of each allele should be input separately in cell A2 to A3, and the inferred mixing pattern and mixing ratio will then be presented in cell E2 to E5. If the detected locus has three alleles, the sequencing depth of each allele should be input separately in cell A8to C8, and the resultswill be presented in cell D8 to E10.

In table “mixing ratio of 3 contributors”, the sequencing depth information should be input in cell A3to C3 (for locus of 3 alleles), A35to D35 (for locus of 4 alleles), A60to E60 (for locus of 5 alleles), the results will be accordingly presented in A6 to B31,A38 to B56,A63 to B68.

If no mixing pattern and mixing ratio could explain the sequencing depth, the results will be displayed as “False”.

Notes:

1. The total sequencing depth for a locus should be 1000. If not, reduce to 1000 based on the proportion of each allele before inputting.

2. the sequencing depth of each allele should be input from the smallest to the largest.

3. The inferred mix ration will be presented in this way: 1 : X ( 1≤X) or 1 : X : Y ( 1≤x≤y ).

4. The mixing patterns will be presented through a code. In the alphabeticpart of the code, “HE” means the individual is a heterozygote in detected locus. And “HO” means homozygote. The contributors are ranked according to the DNA amount from lowest to largest. For a two-person mixture, HEHO and HOHE are two different situations. In the numerical part of the code, each number indicates the amounts of shared alleles between individuals. If it is a mixture of two, the code will have only one number indicating the number of shared alleles. But in a mixture of three, for example, “HEHEHE0000”,the first ”0” indicates 0 allele is shared by the three contributors, the second “0” indicates 0 allele is shared by the first and second contributors, the third “0” indicates 0 allele is shared by the first and third contributors,the last “0” indicates 0 allele is shared by the second and third contributors.