Display Settings:

Items per page
We are sorry, but NCBI web applications do not support your browser and may not function properly. More information

Results: 7

1.
Figure 4.

Figure 4. From: Low-coverage sequencing: Implications for design of complex trait association studies.

Genotype calling pipeline for the 1000 Genomes Pilot 1 Project. The pipeline we have developed to call genotypes for individuals sequenced at an average depth of ∼4–5× by the 1000 Genomes Pilot 1 Project.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
2.
Figure 3.

Figure 3. From: Low-coverage sequencing: Implications for design of complex trait association studies.

Genotype concordance and fraction of genotypes by non-ancestral allele counts (60 individuals sequenced at 4×). Genotype concordance (y-axis on left, dots) and fraction of genotypes (y-axis on right, bars) for simulated data, broken down by genotype category (homozygotes for the ancestral allele [HomRef], heterozygotes [Het], and homozygotes for the non-ancestral allele [HomAlt]) are plotted as a function of non-ancestral allele count among 60 individuals sequenced at 4× (x-axis).

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
3.
Figure 1.

Figure 1. From: Low-coverage sequencing: Implications for design of complex trait association studies.

SNP discovery (%) by MAF, sequencing depth, and sequencing sample size. We simulated 30–2000 individuals sequenced at depths 2×, 4×, 6×, and 30×. We plotted the % of SNPs discovered by population MAF category (<0.1% to >5%), where population MAF is for the 45,000 simulated chromosomes. The dotted lines show the % of SNPs in each population MAF category that is polymorphic among the sequenced individuals.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
4.
Figure 5.

Figure 5. From: Low-coverage sequencing: Implications for design of complex trait association studies.

SNP detection power by minor allele count. For both simulated CEU and real data sets from the 1000 Genomes Project, SNPs were detected through a joint analysis of 59 or 60 individuals. Power of SNP detection was evaluated using a subset of 43 individuals.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
5.
Figure 6.

Figure 6. From: Low-coverage sequencing: Implications for design of complex trait association studies.

Genotype calling quality: Simulated versus the 1000 Genomes Pilot 1. Genotype calling quality is gauged by two measures—genotypic concordance and dosage r2—by comparing with true genotypes in simulated data and with experimental genotypes in real data from the 1000 Genomes Low-coverage Pilot Project. For both the real and simulated data, 60 individuals were sequenced at an average depth of 4×. For the 1000 Genomes Pilot 1 data, genotype calling was performed using sequencing data alone without HapMap 3 genotypes.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
6.
Figure 2.

Figure 2. From: Low-coverage sequencing: Implications for design of complex trait association studies.

Genotype calling quality by MAF, sequencing depth, and sequencing sample size. We simulated 30–2000 individuals sequenced at depths 2×, 4×, and 6×. We compared genotype calls at detected SNPs with the simulated truth to obtain two measures of genotype calling quality, genotypic concordance and dosage r2, for each called SNP. We plot these two measures (left panel: genotypic concordance; right panel: dosage r2) by population MAF category (<0.1% to >5%), where population MAF is for the 45,000 simulated chromosomes.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.
7.
Figure 7.

Figure 7. From: Low-coverage sequencing: Implications for design of complex trait association studies.

Power of association mapping by sequencing depth and number of individuals sequenced. We simulated 1500 cases and 1500 controls, assuming a single causal variant with causal allele frequency 0.5%, 1%, or 3%. We sequenced all 3000 individuals or a random subset of 400, 1000, or 2000 individuals (equal number of cases and controls) at depths ranging from 2×–30×. Power was estimated using an empirical threshold determined from 500 null sets to ensure familywise type-I error of 5%.

Yun Li, et al. Genome Res. 2011 June;21(6):940-951.

Display Settings:

Items per page

Supplemental Content

Recent activity

Your browsing activity is temporarily unavailable.

Write to the Help Desk