| Autor: |
Ardalan Naseri, Kecong Tang, Geng, Xin, Junjie Shi, Zhang, Jing, Pramesh Shakya, Xiaoming Liu, Shaojie Zhang, Zhi, Degui |
| Rok vydání: |
2021 |
| Předmět: |
|
| DOI: |
10.6084/m9.figshare.14053332.v1 |
| Popis: |
Additional file 1: Figure S1. The probability distributions of the sum of genetic lengths shared among pairs of individuals in five types of relatedness using detected IBD segments by RaPID. Figure S2. Number of IBD calls for different IBD detection tools using chromosome 22 of 200K individuals from UK Biobank. Figure S3. An example of IBD segments over chromosome 12 called by different methods using a twin pair. Figure S4. Average detection power of different methods for twins on all autosomes. Figure S5. Ethnicity by ethnicity kinship matrix using the self-reported ethnic backgrounds in UK Biobank and the sum of detected IBD segments by RaPID in all autosomes. Figure S6. Relative count of British individuals. Figure S7. Cross-region average relative count. Numbers are normalized by total potential pairs and the total length of the chromosomes. Figure S8. Percentage of the genome covered by IBD segments from others in UK Biobank by ethnicity. Figure S9. Average percentage coverage of chromosome 1 by IBD segments after filtering out detected IBD segments. Figure S10. Genome coverage of individuals by IBD segments in the UK Biobank data for chromosome 1. Figure S11. Number of relatives sharing 5-10 cM vs. sharing 10 cM IBD segments for individuals in UK Biobank after filtering RaPID results. Figure S12. The distribution of REIN of all UK Biobank participants within 1, 5, 10, and 25 km radius. Figure S13. Preference of local connectivity as measured by relative enrichment in the neighborhood (REIN) after filtering RaPID results. Figure S14. Correlation between the preference of local connectivity (enrichment of relatives in a 25 km neighborhood, e25) and population density (neighbor count). Table S1. IBD results of Germline, iLash, Refined IBD, and RaPID (rows) covered by other tools (columns). Table S2. Average detection power of different methods. Table S3. Accuracy of called IBD segments using MZ twin pairs. Table S4. Average mismatch rate and parent coverage of IBDs in trios using different methods. Average parent coverage denotes the proportion of the IBD segments from child-other that were overlapping by parent-other segment. Table S5. Parent coverage of IBDs in trios using different methods where parents are not used for phasing the genotype data. Table S6. Relative enrichment in different neighborhoods decays with increasing radius. Table S7. Enrichment of people with different local connectivities in UK areas, as indicated by Pearson’s residuals. Table S8. Parameters and command lines for benchmarking different IBD detection tools. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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