目录
遗传结构和遗传多样性分析内容整理
参考路径 /NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/SNP/zhangxin
1 核苷酸多样性
使用软件Vcftools ：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/population
参考路径：
/NJPROJ3/RNA_SH/software/vcftools_0.1.13/cpp/vcftools --vcf final.vcf --keep ZZJ --recode --recode-INFO-all --out ZZJ #final.vcf 是包含所有样品的vcf 文件，这一步旨在按照种群对vcf 进行拆分 /NJPROJ3/RNA_SH/software/vcftools_0.1.13/cpp/vcftools --vcf ZZJ.recode.vcf --window-pi 1000 --out ZZJ_nucleotide_diversity #计算种群核苷酸多样性，1000bp 为一个滑窗
2 .Arlequin 软件计算遗传结构
1） 将vcf 文件转换为.arp 文件，即Arlequin 软件的输入文件。
参考路径：/TJPROJ1/RNA/shouhou/personal_dir/wangbaojian/xuexi/arlequin-3.5.2.2/setup/baidoushan_shenfen
篦子项目路径：
/NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/gexinghua/Arlequin
/TJPROJ6/RNA_SH/shouhou/gexinghua/X101SC19110580/Arlequin
perl /NJPROJ1/PAG/Crop/share/pipeline/GWAS/pipeline/Population/bin/02.TREE/vcf2popsnp.v3.pl final.vcf out_dir perl GenoToArp_2.pl -i baidoushan.geno -idgroup group -size 13545 -misrate 0.02 -maf 0.05 -o shenfen.arp
2）准备.ars 文件（保存Arlequin 分析的参数文件，可以由win版本的Arlequin 软件输出，也可以直接用我已经设置好的.ars 文件）
/TJPROJ6/RNA_SH/software/arlequin/arlecore3522_64bit shenfen.arp shenfen.ars
这部分结果会生成shenfen.res 文件夹，找到shenfen.xml 文件，本次分析的相关结果都可以在这里面找到。
期望杂合度（He） 和观测杂合度（Ho） 统计结果，表格最后会有平均值。
-------------------------------------------------
Num.
gene Num. Obs. Exp.
Locus# copies alleles Het. Het
-------------------------------------------------
1 46 2 0.34783 0.46377
2 64 2 0.34375 0.28919
3 64 2 0.34375 0.28919
两两种群fst 值统计：
<PairFstMat time="08/04/19 at 15:10:49">
Distance method: Pairwise differences
1 2 3 4
1 0.00000
2 0.17423 0.00000
3 0.25449 0.26326 0.00000
4 0.29934 0.28930 0.33585 0.00000
AMOVA分析结果
---------------------------------------------------------------------- Source of Sum of Variance Percentage variation d.f. squares components of variation ---------------------------------------------------------------------- Among populations 3 4836.469 31.26725 Va 23.66 Within populations 212 21392.045 100.90587 Vb 76.34 ---------------------------------------------------------------------- Total 215 26228.514 132.17312 ---------------------------------------------------------------------- Fixation Index FST : 0.23656 ----------------------------------------------------------------------
3. structure 分析
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/STRUCTURE
篦子项目路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/gexinghua/structure
最新structure结果位置:
/NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/legacy/gatk_dp10_structure/structure
使用/NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/legacy/gatk_dp10_structure/snp-dp10-miss0.5-maf0.05_DPmin10.vcf.all
脚本路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/script/Structure
4. PCA 分析
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/PCA
篦子项目路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/X101SC19110580/gexinghua/pca
脚本路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/script/pca/PCA.sh
5.Tree 分析
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree
脚本路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/script/02.TREE
perl /NJPROJ1/PAG/Crop/share/pipeline/GWAS/pipeline/Population/bin/02.TREE/vcf2popsnp.v3.pl final.vcf /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan zcat /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.geno.gz > /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.geno perl /NJPROJ1/PAG/Crop/share/pipeline/GWAS/pipeline/Population/bin/02.TREE/getInfo_treebest.pl /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.geno /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/STRUCTURE/samplelist /NJPROJ1/PAG/Crop/share/software/PopEvolution/software/treebest-1.9.2 nj -b 1000 rmRef.fa >/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.nj_tree.out perl /NJPROJ1/PAG/Crop/share/pipeline/GWAS/pipeline/Population/bin/02.TREE/tree4plot.pl /NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.nj_tree.out NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/Tree/baidoushan.nj_tree.out.result
6 .选择性消除分析
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/select/pi_fst
脚本路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_genetic_diversity/select/script
7. IBD_Mantel 检验
软件及相关输入输出文件备份（windows）：/NJPROJ3/RNA_SH/software/IBD_1.53_for_Windows.zip
输入文件格式： GENETIC_DISTANCE 两两种群的Fst/(1-Fst) ;两两种群的地理遗传距离 GEOGRAPHIC_DISTANCE。
GENETIC_DISTANCE 1 2 0.5763 1 3 0.6375 1 4 0.4285 1 5 0.413 1 6 0.4442 1 7 0.4322 1 8 0.5276 1 9 0.0058 1 10 0.7234 2 3 0.7275 2 4 0.1845 2 5 0.1587 2 6 0.1925 2 7 0.2168 2 8 0.5977 2 9 0.5324 2 10 0.6797 3 4 0.548 3 5 0.5139 3 6 0.5454 3 7 0.5354 3 8 0.2468 3 9 0.6207 3 10 0.7234 4 5 0.0921 4 6 0.0036 4 7 0.1237 4 8 0.4423 4 9 0.398 4 10 0.5348 5 6 0.097 5 7 0.1278 5 8 0.3915 5 9 0.3811 5 10 0.4718 6 7 0.1157 6 8 0.4286 6 9 0.4099 6 10 0.5107 7 8 0.4508 7 9 0.3975 7 10 0.4736 8 9 0.5072 8 10 0.5857 9 10 0.659 GEOGRAPHIC_DISTANCE 1 2 561.82 1 3 461.04 1 4 544.51 1 5 541.46 1 6 538.84 1 7 450.42 1 8 447.03 1 9 5.72 1 10 427.19 2 3 1022.35 2 4 51.91 2 5 25.04 2 6 54.76 2 7 134.19 2 8 1008.23 2 9 567.54 2 10 969.77 3 4 1005.47 3 5 1002.33 3 6 999.79 3 7 910.63 3 8 14.33 3 9 455.33 3 10 205.92 4 5 33.85 4 6 5.76 4 7 98.72 4 8 991.5 4 9 550.22 4 10 943.39 5 6 34.63 5 7 109.26 5 8 988.25 5 9 547.18 5 10 947.13 6 7 92.99 6 8 985.82 6 9 544.54 6 10 937.63 7 8 896.75 7 9 456.09 7 10 844.9 8 9 441.32 8 10 203.79 9 10 421.95
表达多样性分析内容
1 .Ed 和Ep 计算结果
根据文献中提供的公式，Ep 即种群fpkm 的平均值，Ed 种群| 每个样品的fpkm - Ep| 的累加值/（n-1）.Ep .
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_expression_diversity/population
2. Anova 方差分析
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_expression_diversity/Anova
3. KS 检验
方法见：https://www.cnblogs.com/arkenstone/p/5496761.html
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_expression_diversity/KS
4. 相关性分析
主要是计算Ed ,Ep等表达相关多样性和遗传多样性之间的相关性，涉及到的方法也是皮尔森相关和Mantel 检验
参考路径：/NJPROJ3/RNA_SH/shouhou/gexinghua/beifen/tmp/P101SC18061879/gexinghua_expression_diversity/EpvsGeneticvsGeographic
