Extra Supplementary Information

Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources

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Real-life scenario: the 1000 Genomes Project. This section contains the figures for principal component analysis and the output results from IPCAPS.
Simulated data set used to find the optimal Fixation Index as Threshold for fine-scale structure.
Complex simulated data set

Real-life scenario: the 1000 Genomes Project

IPCAPS subtyping resulted in 24 groups (excluding the outliers). Figure 1 shows the first 3 principal components of all samples including the outliers with populations as labels. Figure 2 shows the first 3 principal components of all samples excluding the outliers with populations as labels. Figure 3 show the first 3 principal components of all samples excluding the outliers with the IPCAPS clusters as labels. For the result file, it consists of 28 columns (Table 1). The fist 3 columns are individual IDs, population labels, assigned clusters, and the first 25 principal components. The full result table can be downloaded from here.

Figure 1: the first 3 principal components of all samples including the outliers with populations as labels.

Figure 2: the first 3 principal components of all samples excluding the outliers with populations as labels.

Figure 3: the first 3 principal components of all samples excluding the outliers with the IPCAPS clusters as labels.

Individual	Population	Cluster	PC1	PC2	PC3
individual1	GBR	22	-0.0107380574672092	0.027763112230486	-0.0128725996586141
individual2	GBR	22	-0.0106240572135524	0.0276327017132276	-0.0122091313249076
individual3	GBR	22	-0.0110723121500444	0.0270967793266127	-0.0113694771754151
individual4	GBR	22	-0.0109009970688707	0.0277297792670736	-0.0125973983735742
individual5	GBR	22	-0.0109107684428465	0.0271314604934395	-0.0127706893426669
individual6	GBR	22	-0.011440781490344	0.0271660498293538	-0.0116799608060983
individual7	GBR	22	-0.0109098385167301	0.0271773381154484	-0.0118470043335346
individual8	GBR	22	-0.0107978960499085	0.027178628903619	-0.0123339836623878
individual9	GBR	22	-0.0107669661943635	0.0275825096725119	-0.0109637054008316

Table 1: The first nine rows and the first six columns of the result table from the 1000 Genomes Project.

Simulated data set for the optimal Fixation Index

As we explained in the supplementary section S3 (see ), we simulated 100 replicates of one population with 5,000 SNPs and 500 individuals. Figure 4 shows the first 3 principal components of one of 100 simulated data set with this setting.

Figure 4: the first 3 principal components of one population with 5,000 SNPs and 500 individuals.

The simulated data files are provided in the PLINK format, which can be downloaded from:

Complex simulated data set

We simulated a complex data set consisting of 15 populations, 2000 individuals, and 5,000 SNPs. The pair-wise Fst (Fixation Index) distances for all populations are shown in Table 2. Figure 5 shows the first 3 principal components of this complex simulated data set. For the result, the IPCAPS detects 15 clusters (see Figure 6). For the accuracy of IPCAPS on this complex data set, it can be calculated using Adjusted Rand Index (ARI) as

library(mclust)
groups <- read.delim("sim_complex_data/IPCAPS_groups.txt")
ari <- adjustedRandIndex(groups$group, groups$label)
print(ari)

## [1] 0.9077214

Note: The IPCAPS result can be downloaded from here

	pop2	pop3	pop4	pop9	pop6	pop7	pop8	pop10	pop11	pop12	pop13	pop14	pop15
pop1	0.002	0.004	0.005	0.220	0.220	0.222	0.223	0.215	0.214	0.216	0.216	0.216	0.216
pop2		0.004	0.005	0.220	0.221	0.223	0.223	0.216	0.214	0.217	0.217	0.216	0.216
pop3			0.007	0.222	0.223	0.224	0.225	0.219	0.217	0.220	0.219	0.219	0.219
pop4				0.221	0.222	0.224	0.224	0.217	0.215	0.218	0.218	0.217	0.217
pop9					0.002	0.003	0.005	0.216	0.217	0.219	0.218	0.218	0.218
pop6						0.003	0.005	0.216	0.216	0.219	0.218	0.218	0.218
pop7							0.006	0.218	0.219	0.221	0.220	0.220	0.220
pop8								0.219	0.220	0.222	0.221	0.221	0.221
pop10									0.003	0.005	0.004	0.005	0.003
pop11										0.005	0.004	0.005	0.003
pop12											0.006	0.007	0.005
pop13												0.006	0.004
pop14													0.005

Table 2: The pair-wise Fst (Fixation Index) distances simulated populations.

Figure 5: the first 3 principal components of the complex simulated data set.

Figure 6: the first 3 principal components of the IPCAPS results.

The simulated data files are provided in the PLINK format, which can be downloaded from: